Due to the short shelf life of raw milk, humans have developed a variety of fermentation and preservation techniques to prolong milk’s nutritional quality. One of these techniques is the fermentation of milk with small aggregates of bacteria and yeast known as kefir grains. While fermentation is normally thought about from the perspective of sugar metabolism, a study recently carried out by our group demonstrated that fermenting bovine milk with kefir grains also led to significant degradation of endogenous milk peptides. Using mass spectrometry (ESI-Orbitrap MS/MS), thousands of peptides were identified in both fermented and unfermented bovine milk, with many new peptides identified in the fermented samples. With careful use of controls, we demonstrated that milk peptides and proteins are cleaved by the kefir bacteria themselves, as opposed to other factors that may be introduced as part of the traditional fermentation process. The fermented milk samples contained a variety of peptides known to be functional, including some with antibacterial, opioid, and antioxidant functions.