Increased consumption of yogurt, kefir, and other fermented foods has been driven, in part, by the health benefits these products may confer. Epidemiological studies have shown that the consumption of fermented foods is associated with reduced risks of type 2 diabetes, metabolic syndrome, and heart disease, along with improved weight management. The microorganisms present in these foods are suggested to contribute to these health benefits. Among these are the yogurt starter culture organisms Streptococcus thermophilus and Lactobacillus delbrueckii subsp bulgaricus as well as Bifidobacterium and Lactobacillus strains that are added for their probiotic properties. In contrast, for other fermented foods, such as sauerkraut, kimchi, and miso, fermentation is initiated by autochthonous microbes present in the raw material. In both cases, for these fermentation-associated microbes to influence the gut microbiome and contribute to host health, they must overcome, at least transiently, colonization resistance and other host defense factors. Culture and culture-independent methods have now clearly established that many of these microbes present in fermented dairy and nondairy foods do reach the gastrointestinal tract. Several studies have shown that consumption of yogurt and other fermented foods may improve intestinal and extraintestinal health and might be useful in improving lactose malabsorption, treating infectious diarrhea, reducing the duration and incidence of respiratory infections, and enhancing immune and anti-inflammatory responses.