Your gut health does not only impact your digestive system. What’s going on in your gut plays a role in everything from your immune system to your mental health and brain function—so filling your plate with foods that support your gut health is crucial. Two of the most popular are yogurt and kefir, both of which are fermented dairy foods. But if you pit them against each other, yogurt vs. kefir, is one of them better for your gut health than the other?
Meet the experts: Trisha Pasricha, M.D., a gastroenterologist, assistant professor at Harvard Medical School and author of You’ve Been Pooping All Wrong; Supriya Rao, M.D., a gastroenterologist with Integrated Gastroenterology Consultants in Lowell, MA.
Here, gastroenterologists share the benefits of yogurt and kefir, plus how to incorporate them into a gut-healthy diet.
Yogurt vs. kefir: Nutrition
Here’s how these two fermented dairy products compare from a nutrition perspective.
Yogurt nutrition
According to the U.S. Department of Agriculture (USDA), 100 grams (g) or about half a cup of plain, nonfat Greek yogurt contains:
- 59 calories
- 10.3 g of protein
- 0.4 g of fat
- 3.6 g of carbohydrates
- 3.3 g of sugar
Kefir nutrition
Per the USDA, 100 g or ½ cup of plain, low-fat kefir contains:
- 43 calories
- 3.8 g of protein
- 1 g of fat
- 4.8 g of carbohydrates
- 4.6 g of sugar
Yogurt benefits
The first thing you need to know about yogurt is that if you want to maximize the potential health benefits, you must choose Greek. “Greek yogurt can absolutely be part of a gut-healthy diet,” says gastroenterologist Trisha Pasricha, M.D., an assistant professor at Harvard Medical School and author of You’ve Been Pooping All Wrong. “I often point out that Greek yogurt contains almost twice the protein of regular yogurt, which can make it a satisfying and nutritious food.” While the protein is filling, energizing, and makes yogurt a satisfying base for a meal, there are also other nutrients in yogurt that support gut health.
“Yogurt contains calcium and probiotics, which are beneficial bacteria that can help support your gut microbiome,” explains Supriya Rao, M.D., a gastroenterologist with Integrated Gastroenterology Consultants in Lowell, MA. “These bacteria can aid digestion and may help with issues like mild bloating or diarrhea.” These perks have been well documented. One study in BMC Microbiology found that eating yogurt induces positive changes in the gut microbiome, plus may contribute to reductions in visceral fat mass, while another study in The Journal of Nutrition found that eating probiotic-rich yogurt had a stronger impact on the gut microbiome than just eating prebiotic foods like oats.
“For people who have trouble tolerating lactose, yogurt is usually easier to digest than milk because of the fermentation process which breaks down some of that lactose,” says Dr. Rao. However, some folks with lactose intolerance may still experience symptoms from eating yogurt.
Potential downsides of yogurt
While yogurt can be very beneficial for gut health, “the key is choosing the right kind of yogurt,” Dr. Pasricha says. “Many yogurts have become ultra-processed foods. The ideal Greek yogurt should really contain just two ingredients: milk and cultures.” That’s why checking the ingredient list before selecting a yogurt is so important. “Many flavored yogurts add artificial sweeteners, stabilizers, or thickeners like guar gum or corn starch to create that perfectly creamy texture. These additives can sometimes disrupt digestion or irritate the bowels,” Dr. Pasricha explains. Dr. Rao adds that many flavored yogurts can be high in added sugars as well.
“My preference is plain, low-fat Greek yogurt, which keeps saturated fat in check,” says Dr. Pasricha. “Then you can flavor it yourself with things like berries, honey, or granola, which gives you more control over what you’re putting into your body.”
Kefir benefits
If you’ve never tried kefir, you can find it in the dairy aisle right next to the yogurt. “Kefir is a fermented dairy product and usually contains a much wider range of probiotic bacteria and yeast than yogurt,” says Dr. Rao. Tangy and drinkable, kefir contains lactic acid bacteria, acetic acid bacteria, yeasts, and fungi, all of which contribute to a more diverse microbiome. According to research in the journal Foods, kefir has been linked to anti-carcinogenic, anti-hypertensive, and anti-diabetic effects.
“Kefir also has less lactose than yogurt because it is fermented longer, so it’s great for those who can’t tolerate milk but still want those benefits,” Dr. Rao says. Kefir contains less protein than Greek yogurt, but because it’s a drink it is often enjoyed as a snack or alongside a meal, so the satiety factor that protein-rich Greek yogurt provides is not as necessary.
All told, a 2026 review in Frontiers in Food Science and Technology found that kefir supports the digestive system and immune system, plus fights inflammation to help support a healthy gut microbiome.
Potential downsides of kefir
There aren’t many downsides to enjoying kefir, Dr. Rao says. “Kefir has a tangy flavor and thinner texture that some folks may not like but otherwise it’s a go-to for me to support gut health.” That said, as is the case with yogurt, you need to be aware of added sugars in flavored varieties. “Added sugar can cancel out some of the health benefits,” says Dr. Rao.
Yogurt vs. kefir: Which is better for gut health?
Both yogurt and kefir contain beneficial probiotics and other nutrients that support gut health. But if Dr. Rao had to choose one, she would pick kefir. “With kefir, you might get a larger mix of probiotic organisms,” she says. “But honestly, choose the one you like!” Yogurt can be the base for a meal, while kefir is a tangy and delicious sip or snack. As long you are keeping added sugars to a minimum, both are excellent additions to a gut-healthy diet.
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