Bioactive peptides are low molecular weight protein fragments of 2-20 amino acids residues that exhibit beneficial physiological effects in vivo. The generation of bioactive peptides during the manufacture of fermented foods is well documented. These peptides are released from the precursor proteins during fermentation or ripening processes by endogenous or microbial enzymes derived from starter or nonstarter cultures. The production of bioactive peptides in fermented foods is of great interest since they show several interesting bioactivities related to health promotion, such as antihypertensive, opioid, antioxidant, immunomodulating, mucin-stimulating, insulin-mimetic, and antiosteoporotic, among others. Increased yields of bioactive peptides in fermented foods may be achieved by several approaches, including the selection of high proteolytic microorganisms, the suitable combination of co-cultures, optimization of processing conditions, and addition of media-components. In this chapter, the most recent investigations supporting the potential health benefits of bioactive peptides in fermented foods on cardiovascular, nervous, gastrointestinal and immune systems, as well as on bones and adipose tissue are reviewed.