As the leaves begin to turn and the air gets crisp, there’s nothing quite like the comforting aroma of freshly baked pumpkin. Dive into the cozy flavors of autumn with these **healthy pumpkin muffins**! Perfectly soft, wonderfully moist, and sweetened just right, they’re the ideal treat to brighten your mornings or satisfy your afternoon cravings. Whip up a batch for a convenient, wholesome breakfast or a delightful snack to enjoy throughout your week.
Finding yourself with extra pumpkin puree after making these delicious muffins? Don’t let it go to waste! Explore more of our favorite pumpkin-infused delights. For a quick indulgence, don’t miss our single-serve pumpkin mug cake, or create a truly special brunch with these fluffy pumpkin pancakes. We promise, you’ll love every pumpkin-packed bite!

The Ultimate Healthy Pumpkin Muffin Recipe for Everyday Enjoyment
Welcome to the heart of pumpkin season, or simply anytime you’re craving that comforting flavor! You’ve just stumbled upon one of Fit Foodie Finds’ most popular and utterly delicious healthy muffin recipes. This particular healthy pumpkin muffin recipe isn’t just easy to bake; it’s a true testament to how satisfying and wholesome a treat can be. Crafted with simple, nourishing ingredients, these muffins deliver on taste without compromising your health goals. Whether you’re a seasoned baker or just starting your journey in the kitchen, this recipe is designed for success, pure enjoyment, and makes meal prepping a breeze.
While muffins offer convenient individual portions, we understand that sometimes a larger, sliceable bake is preferred. If you lean more towards a loaf, be sure to explore our healthy pumpkin bread recipe. It shares many of the delightful qualities of these muffins – the warm spices, natural sweetness, and moist texture – simply baked in a loaf pan for a different presentation and easy slicing.
Why You’ll Fall in Love with These Healthy Pumpkin Muffins:
These aren’t just any pumpkin muffins; they’re thoughtfully designed to be both delicious and nutritious. Here’s what makes them stand out:
- **100% Whole Grain Goodness:** We use whole wheat flour, ensuring you get all the fiber and nutrients found in the entire grain, contributing to sustained energy and digestive health.
- **Naturally Sweetened Perfection:** Say goodbye to refined sugars! These muffins get their perfect sweetness from wholesome sources like maple syrup and coconut sugar, providing a richer, more nuanced flavor.
- **Made with Wholesome Fats:** Instead of butter, we opt for coconut oil, which contributes to a delicate texture and a source of medium-chain triglycerides (MCTs).
- **Effortlessly Freezer-Friendly:** Prepare a larger batch and freeze them! They thaw beautifully, making them ideal for grab-and-go breakfasts or quick snacks whenever a craving strikes.
- **Incredibly Moist & Flavorful:** Thanks to the pumpkin puree and careful ingredient balance, these muffins are guaranteed to be wonderfully soft, tender, and bursting with the warm, inviting spices of autumn.
Expand Your Muffin Repertoire!
6 Healthy Muffin Recipes from 1 Versatile Base Batter
Are you a true muffin enthusiast, constantly on the hunt for delicious and wholesome recipes? You’re in the right place! We’ve developed a fantastic base recipe that allows you to create a remarkable variety of healthy muffins with minimal fuss. This versatile batter is your secret weapon for endless muffin possibilities. Discover our top 6 healthy muffin recipes, all stemming from one simple, adaptable base. Get all 6 healthy muffin recipes HERE and ensure your kitchen is always filled with delicious, nutritious baked goods!

- Healthy Banana Nut Muffins
- Healthy Chocolate Muffins
- Cranberry Orange Muffins
- Apple Cinnamon Muffins
- Chocolate Pumpkin Zucchini Muffins
- Chocolate Chip Pumpkin Muffins

Essential Insights: Everything You Need to Master Healthy Pumpkin Muffins
Crafting the perfect healthy pumpkin muffin is all about understanding your ingredients and mastering a few simple techniques. This section will guide you through customizing your muffins with delightful mix-ins and provide clever substitutions to ensure baking success every time, even if your pantry isn’t fully stocked.
Customizing Your Muffins: Creative & Delicious Mix-ins
These healthy pumpkin muffins are a fantastic canvas for your culinary creativity! The possibilities for delicious mix-ins are virtually endless, allowing you to tailor each batch to your specific preferences, dietary needs, or simply what you have on hand. Don’t hesitate to experiment and make them uniquely yours!
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Crunchy Nuts for Texture and Flavor:
Incorporating nuts is an excellent way to introduce delightful crunch, a satisfying bite, and an extra layer of earthy flavor to your muffins. To ensure they distribute evenly throughout the batter and don’t sink to the bottom during baking, it’s best to chop them into smaller pieces. Consider these fantastic chopped nut add-ins:
- Walnuts: A classic and beloved pairing with pumpkin, offering rich, earthy notes that enhance the overall spice profile.
- Pecans: Buttery and inherently sweet, pecans complement the warm spices beautifully, adding a touch of indulgence.
- Pistachios: For a slightly unexpected, vibrant green color and a unique, mildly sweet flavor that stands out.
- Almonds: Mild and incredibly versatile, slivered or chopped almonds provide a delicate crunch without overpowering the pumpkin flavor.
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Sweet Chocolate Chips for Indulgence:
Who can resist a touch of chocolate? Adding chocolate chips instantly transforms these healthy muffins into a more decadent treat or a dessert-worthy delight. Dark chocolate chips can add a rich, slightly bitter contrast, while milk chocolate offers a sweeter, more comforting profile. Mini chocolate chips work well for even distribution.
Pro Baker’s Tip: For ultimate versatility, you can even divide your batter in half! Mix chocolate chips into one portion and chopped nuts into the other. This way, you get a batch of muffins perfectly suited for a wholesome breakfast, and another batch ideal for an after-dinner indulgence or a special treat!
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Dried Fruits for Chewy Sweetness:
For a burst of concentrated natural sweetness and a pleasant chewy texture, consider adding dried fruits. Raisins, craisins (dried cranberries), or even chopped dried cherries are excellent choices. They contribute to a more complex flavor profile, often reminiscent of a “morning glory muffin,” making them exceptionally satisfying and flavorful for breakfast.
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Nut Butter Toppings for Extra Richness:
Once your healthy pumpkin muffins are baked to golden perfection and have cooled slightly, take them to the next level with a generous drizzle of your favorite nut butter. Almond butter, peanut butter, or cashew butter can add a creamy richness, an extra boost of healthy fats and protein, making them even more filling, flavorful, and utterly irresistible. A sprinkle of sea salt on top can beautifully balance the sweetness!
Smart Swaps: Flexible Ingredient Substitutions
One of the best qualities of this healthy pumpkin muffin recipe is its forgiving nature when it comes to ingredient adjustments. Don’t fret if your pantry isn’t perfectly stocked, or if you simply wish to experiment with different flavors or textures. Below is a comprehensive list of ingredients and reliable substitution options, ensuring you can bake these delicious muffins anytime, anywhere.
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Pumpkin Puree Alternatives:
If you’re out of pumpkin puree or simply want to try a different flavor profile, any of the following fruit or vegetable purees can work beautifully. Just ensure they are unsweetened for the best results, as added sugars can throw off the recipe’s balance:
- Butternut Squash Puree: This is arguably the closest substitute, offering a very similar flavor, color, and texture to pumpkin. It will blend seamlessly into the recipe.
- Applesauce: Adds a natural sweetness and significant moisture. Always opt for unsweetened applesauce to control the sugar content. The flavor will lean more towards apple, but still delicious.
- Mashed Banana: Will result in a slightly sweeter muffin with a distinct banana flavor. This is a great option if you love banana bread flavors. Ensure bananas are very ripe for maximum sweetness and moisture.
- Shredded Zucchini: A fantastic way to add hidden vegetables and moisture! However, it’s crucial to squeeze out as much excess moisture as possible from the shredded zucchini using a clean kitchen towel to prevent a soggy, dense muffin.
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Flour Options:
This recipe has been thoroughly tested and perfected using **white whole wheat flour**. This type of flour offers the nutritional benefits of whole wheat (higher fiber, more nutrients) with a lighter texture and milder flavor, making it an excellent choice for tender muffins. While we highly encourage sticking to it for optimal results, if you decide to experiment with other flours (such as all-purpose flour for a lighter crumb or a gluten-free blend), please let us know your results! Adjustments to liquid might be needed for different flours.
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Oil Substitutions:
Coconut oil provides a lovely richness and contributes to the moist texture of these muffins. If you don’t have coconut oil on hand, or prefer an alternative, you have several options:
- You can often substitute with an extra 1/4 cup of pumpkin puree for a lower-fat option, but be mindful of the added moisture.
- Alternatively, use other neutral-flavored oils such as **vegetable oil**, **canola oil**, or a light-tasting **olive oil**.
- Melted **unsalted butter** can also be used if you are not strictly dairy-free; it will add a rich, buttery flavor.
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Sweetener Alternatives:
We adore the complex, caramel-like sweetness that coconut sugar and maple syrup impart to these muffins, contributing depth of flavor beyond just sweetness. However, feel free to switch things up based on availability or preference:
- You can substitute **honey** for the maple syrup, keeping in mind that honey is generally sweeter than maple syrup, so you might consider slightly reducing the amount.
- Swap **light or dark brown sugar** for the coconut sugar for a similar depth of flavor and moisture retention.

Frequently Asked Questions About Baking Perfect Pumpkin Muffins
How can I ensure my muffins are consistently fluffy and light?
Achieving that desired fluffy and light muffin texture largely depends on two critical factors: using the correct leavening agent and employing proper mixing technique. For this healthy pumpkin muffin recipe, it’s crucial to use **baking soda** (not baking powder). Always double-check that your baking soda is fresh and not expired; an inactive leavening agent is the quickest path to flat, dense muffins. The most important tip, however, is to **avoid overmixing** the batter. Mix just until the dry and wet ingredients are barely combined. A few small lumps are perfectly fine and even desired; overmixing develops gluten too much, leading to a tough, chewy, and dense texture instead of a tender crumb.
Are muffin liners a necessity, or can I bake directly in the pan?
Muffin liners are certainly convenient and contribute to easier cleanup, but they are not always strictly necessary. If you possess a high-quality non-stick muffin pan that you’ve thoroughly sprayed with non-stick cooking spray (or buttered and floured), you might be able to skip them. However, if you’re concerned about your muffins sticking to the pan, or if you simply prefer a more professional, tidy appearance for your baked goods, using muffin liners is always the safer and recommended bet. They also make the muffins easier to transport and serve.
How long does canned pumpkin puree stay fresh once opened?
Yes, pumpkin puree, once opened, does have a limited shelf life. After opening a can of pumpkin, it’s essential to transfer any unused puree into an airtight container. Store this container promptly in the refrigerator, where it will typically remain fresh and safe to use for about 5-7 days. For unopened canned pumpkin stored in your pantry, always refer to the ‘best by’ or ‘expiration date’ printed on the can. The ‘best by’ date is primarily a manufacturer’s recommendation for peak quality. If it looks, smells, and tastes normal (no mold, off-color, or sour odor), it’s likely still good past this date. However, if it’s past the ‘expiration date,’ it’s safest to discard the contents. Remember to rinse out the can and recycle it!
Can I freeze pumpkin puree for future baking projects?
Absolutely! Freezing pumpkin puree is an excellent and efficient way to preserve it, whether you’ve used store-bought canned pumpkin or prepared homemade puree from scratch. We highly recommend portioning the pumpkin puree into freezer-safe glass containers, silicone molds (then transfer to a bag), or reusable plastic bags. When using bags, ensure you remove as much air as possible before sealing to prevent freezer burn. Properly frozen pumpkin puree can be stored in the freezer for up to 6 months, ready to be thawed and incorporated into your next delicious recipe, ensuring you have pumpkin available year-round.
Freezing Your Healthy Pumpkin Muffins: A Handy Guide for Meal Prep
These healthy pumpkin muffins are absolutely perfect for batch baking and freezing, ensuring you always have a wholesome, homemade snack or breakfast on hand. Freezing them correctly will maintain their delicious flavor and moist texture for weeks. Here’s a detailed guide on how to freeze them effectively:
- **Allow to Cool Completely:** This is the most crucial step! After baking, transfer your muffins to a wire rack and allow them to cool down entirely to room temperature. This can take an hour or two. Cooling completely prevents condensation from forming inside the storage bag, which can lead to ice crystals and soggy muffins once thawed.
- **Flash Freeze (Optional but Recommended):** For best results and to prevent the muffins from sticking together in the freezer bag, arrange the completely cooled muffins in a single layer on a baking sheet. Place the baking sheet in the freezer for about 30-60 minutes, or until the muffins are firm to the touch.
- **Package Securely:** Once flash-frozen (or simply completely cooled, if skipping the flash freeze), transfer the muffins into a large gallon-sized freezer bag or an airtight freezer-safe container.
- **Remove Air & Seal:** If using a freezer bag, squeeze out as much excess air as possible before sealing it tightly. If using a container, ensure the lid is sealed securely. Removing air helps prevent freezer burn, which can dry out your muffins.
- **Label & Store:** Clearly label the bag or container with the date. Your healthy pumpkin muffins can be safely stored in the freezer for up to 3 months.
- **Thawing & Reheating:** To enjoy your frozen muffins, you have a few options:
- **Room Temperature:** Simply let them thaw on the countertop for a few hours.
- **Microwave:** Gently warm them in the microwave for 30-60 seconds until heated through.
- **Oven:** For a “freshly baked” experience, reheat them in a preheated oven (300°F/150°C) for 5-10 minutes until warmed through and lightly crispy on the outside.

Expert Baking Tips & Tricks for Perfect Pumpkin Baked Goods Every Time
Baking with pumpkin is surprisingly straightforward and immensely rewarding. Pumpkin puree adds wonderful moisture, a beautiful vibrant color, and a subtle earthy sweetness to baked goods. It can even be a clever ingredient to replace some of the oil in recipes, or simply to sneak in an extra serving of nutrient-rich vegetables into your diet!
Here are some invaluable tips and tricks to ensure your pumpkin baking endeavors are always a success, resulting in perfectly moist, flavorful, and tender treats:
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Choose the Right Pumpkin Product:
Always, always use **canned pumpkin puree**, not pumpkin pie filling. This is a critical distinction! Pumpkin pie filling contains added spices, sugars, and sometimes thickeners, which will significantly alter the flavor profile and sweetness balance of your recipe. If a recipe calls for pumpkin puree, it means plain, unsweetened cooked pumpkin. Alternatively, if you have the time and desire, you can also use homemade pumpkin puree for an even fresher taste and control over the consistency.
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Pumpkin as an Oil or Fat Substitute:
A fantastic trick for making many baked goods healthier and lower in fat is to substitute pumpkin puree for some of the oil or butter. The general rule of thumb for this substitution is a **1:1 ratio**. However, since pumpkin adds more moisture than oil, you might need to slightly adjust other liquid ingredients in the recipe (e.g., milk or water) to maintain the right batter consistency. Start by replacing half the oil/butter with pumpkin and adjust from there.
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Don’t Underbake (or Overbake!):
Pumpkin adds a significant amount of moisture to baked goods, which can sometimes create the illusion that an item is fully cooked when it’s not quite there. To ensure your pumpkin muffins or bread are thoroughly baked through, always use the toothpick test: insert a toothpick into the center, and it should come out clean or with moist crumbs, not wet batter. For larger items like loaves, an instant-read thermometer is your best friend: the internal temperature should reach at least **200ºF (98°C)** for doneness. Be careful not to overbake either, as that can lead to dry results.
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Beware of Overmixing the Batter:
This is perhaps the most crucial tip for achieving wonderfully fluffy and tender muffins. When mixing your pumpkin muffin batter, use a light hand. It is highly recommended to mix by hand with a spatula or wooden spoon until just combined. Overmixing develops the gluten in the flour excessively, leading to a dense, tough, and rubbery texture instead of the soft, tender crumb we all love in a good muffin. A few lumps in the batter are perfectly acceptable and even preferred.
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Embrace the Warm Spices:
Pumpkin pairs wonderfully with a medley of warm autumn spices. Don’t be shy with cinnamon, nutmeg, ginger, and cloves. If you have it, using a pre-made or homemade pumpkin pie spice blend is a fantastic shortcut for enhancing the flavor profile and creating that quintessential fall taste.
Transforming Muffins into a Loaf: Easy Bread Directions
If you adore the rich, spiced flavor of these healthy pumpkin muffins but prefer the convenience and sliceability of a bread loaf, this recipe easily converts! Simply follow the main batter preparation instructions as outlined, then adapt the baking process as follows to create a beautiful pumpkin bread:
- **Prepare Your Loaf Pan:** Transfer the entire prepared muffin batter into a standard-size bread pan (typically 9×5 inches). Ensure your pan has been thoroughly greased and lightly floured, or lined with parchment paper, to prevent sticking.
- **Bake with Care:** Place the loaf pan in a preheated oven at **350ºF (175°C)**. The baking time will be longer than for muffins, approximately **45-50 minutes**.
- **Check for Doneness & Prevent Over-Browning:** Around the 30-minute mark, check the bread. If the top and sides are beginning to brown too quickly, loosely tent the loaf with a piece of aluminum foil. This helps to prevent the crust from becoming too dark while allowing the interior to finish baking. The loaf is fully cooked when a wooden skewer or toothpick inserted into the center comes out clean, or an instant-read thermometer reads an internal temperature of 200°F (98°C).
- **Cool Before Slicing:** Once baked, remove the pumpkin bread from the oven. Allow it to cool in the pan for 10-15 minutes before carefully inverting it onto a wire rack to cool completely. This cooling period is essential for the bread to set properly, making it easier to slice without crumbling.
More Seasonal Delights:
Our Favorite Healthy Pumpkin Recipes to Try Next
If you’ve fallen in love with the comforting flavors of these healthy pumpkin muffins, you’ll be thrilled to explore more of our wholesome and utterly flavorful pumpkin creations. Pumpkin is an incredibly versatile ingredient, lending itself beautifully to both sweet and savory dishes, making it a fantastic addition to your cooking year-round. Here are some more healthy pumpkin recipes from our kitchen to yours, perfect for any occasion:
- Healthy Pumpkin Bread: A moist, wonderfully spiced loaf that’s a true classic.
- Homemade Pumpkin Spice: Craft your own perfect blend of warm spices to elevate all your fall baking.
- Pumpkin Oatmeal Bars: Chewy, hearty, and packed with pumpkin goodness – a great snack or dessert.
- Healthy Pumpkin Pie Bars: All the irresistible flavors of traditional pumpkin pie in an easy-to-serve bar form.
- Chocolate Pumpkin Bread: A rich and decadent twist on classic pumpkin bread, with deep cocoa notes.
- Chocolate Chip Pumpkin Bread: For those who love a delightful burst of chocolate in every single bite.
- Pumpkin Cream Cold Brew: A fantastic homemade version of your favorite seasonal coffee shop drink, perfect for a pick-me-up.
Healthy Pumpkin Muffins
These delicious healthy pumpkin muffins are crafted with wholesome white whole wheat flour, natural pumpkin puree, rich maple syrup, and optional walnuts, offering a perfect blend of nutrition and cozy fall flavor!
By: Lee Funke
Overall Rating: 4.93 out of 5 stars (based on 14 votes)
Prep Time: 10 minutes
Cook Time: 21-24 minutes (for muffins) / 45-50 minutes (for loaf)
Total Time: Approximately 55 minutes
Yields: 12 Muffins
Print Recipe
Ingredients
Dry Ingredients
- 1.75 cups white whole wheat flour
- ½ cup coconut sugar
- 1 teaspoon baking soda
- 2 teaspoons ground cinnamon
- ¼ teaspoon nutmeg
- ⅛ teaspoon ground ginger
- ⅛ teaspoon ground cloves
- ⅛ teaspoon salt
- ½ cup chopped walnuts (optional, for mixing into batter)
Wet Ingredients
- 2 large eggs
- ½ cup maple syrup
- 1 cup pumpkin puree (ensure it’s pure, not pie filling)
- ½ cup unsweetened almond milk
- 1 teaspoon vanilla extract
- ¼ cup coconut oil, melted
Instructions
- **Prepare Oven & Muffin Tin:** Begin by preheating your oven to 350ºF (175°C). Line a standard 12-cup muffin tin with muffin liners. For additional non-stick assurance, lightly spray the inside of each liner with cooking spray.
- **Combine Wet Ingredients:** In a large mixing bowl, thoroughly beat the eggs, coconut sugar, and maple syrup together until the mixture is well combined and slightly frothy. Next, stir in the almond milk, pumpkin puree, and vanilla extract until the wet ingredients are smooth and fully incorporated.
- **Combine Dry Ingredients:** In a separate medium bowl, whisk together all the dry ingredients: white whole wheat flour, baking soda, ground cinnamon, nutmeg, ground ginger, ground cloves, and salt. Make sure these are well blended. (Do not add any chopped walnuts to the dry ingredients at this stage.)
- **Gently Combine Wet & Dry Mixtures:** Gradually add the dry ingredient mixture to the wet ingredients in the large bowl. Using a spatula or wooden spoon, mix by hand just until combined. It is crucial not to overmix the batter; a few small lumps are perfectly normal and desired for tender, light muffins.
- **Fold in Mix-ins:** Finally, gently fold in the chopped walnuts (if you are using them as a mix-in) and the melted coconut oil until they are evenly distributed throughout the batter.
- **Fill Muffin Tin & Bake:** Divide the prepared batter evenly among the 12 muffin cups, filling each approximately 3/4 of the way full. This will result in generously sized muffins. If desired, sprinkle a few extra chopped walnuts or chocolate chips on top of each muffin before baking for a beautiful, bakery-style finish. Bake in the preheated oven at 350ºF (175°C) for 21-24 minutes, or until a wooden skewer or toothpick inserted into the center of a muffin comes out clean.
- **Cool Thoroughly:** Once baked, remove the pumpkin muffins from the oven. Allow them to cool in the muffin pan for 5-10 minutes. Then, carefully remove the muffins from the pan and transfer them to a wire rack to finish cooling completely.
- **Serve & Enjoy:** Your healthy pumpkin muffins are now ready to be savored! Enjoy them warm, at room temperature, or save them for later.
Tips & Notes
- This recipe consistently yields 12 delicious, standard-sized muffins.
- If you choose to bake this batter as a loaf, it will typically serve 8-10 slices.
- Nutrition information provided below is an approximation calculated for one of the 12 muffins.
- For Loaf Baking (alternative instructions): To make a pumpkin bread loaf, simply pour the entire batter into a greased 9×5-inch bread pan. Bake at 350ºF (175°C) for approximately 45-50 minutes, or until a toothpick inserted into the center comes out clean. If the top begins to brown too quickly, loosely tent the pan with aluminum foil.
- Always ensure you are using pure pumpkin puree, not pumpkin pie filling, for the best results and flavor balance.
Watch the Recipe Video: Healthy Pumpkin Muffins
For a visual guide to making these delicious and healthy pumpkin muffins, watch our step-by-step recipe video:
This video demonstrates how to make healthy pumpkin muffins using 100% whole wheat flour, pumpkin puree, and maple syrup, achieving a perfect, moist texture.
Nutrition Facts (per 1 muffin serving)
Calories: 227 kcal
Carbohydrates: 33 g
Protein: 4 g
Fat: 9 g
Fiber: 3 g
Sugar: 17 g
Please note: Nutrition information is an automatic calculation based on ingredients and should be used as an approximation. Actual values may vary based on specific brands and preparation methods.
Love this healthy pumpkin muffin recipe? We’d be thrilled to hear your thoughts! Leave a comment below and share your experience with us.
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