Milk kefir (MK) and water kefir (WK) are traditionally produced from different unique probiotic-containing semi-soft particles known as milk kefir grains and water kefir grains. There is significant confusion between these kefir grains, even in peer-reviewed scientific publications. Even though both grains have some similarities, they have significant differences in structure, microbial content, and impact on the finished beverage product. This review compares the two probiotic kefir grains and examines the similarities and differences in these two grains and the products made from them. Microbiological, chemical, and functional properties for two grains are examined. The two different fermented beverages produced from these grains have different physical and chemical characteristics and different microbiological composition. MK and WK also have different functional properties. During the COVID-19 pandemic, the consumption of natural probiotic-containing foods was suggested as beneficial for improving gut health and, consequently, overall health. MK and WK contain broad spectra of probiotic microorganisms, which may help improve overall health and immunity. Consequently, MK and WK may help protect against COVID-19 and especially in the elderly. While milk kefir provides significant amounts of protein as well as probiotics and prebiotics, water kefir can be a significant probiotic and prebiotic source for vegans and people who are allergic to dairy products. Both of these grains are important for their potential health benefits. •Milk kefir and water kefir grains are two unique probiotic starter cultures.•Kefir grains were naturally formed via the symbiotic relationships of inherent microorganisms.•Beverages prepared from these grains are wholly unique among probiotic products.•Each kefir product has significant health promoting properties.•Water kefir has great potential as a probiotic product for those who are allergic to dairy ingredients as well as to vegans.