Over decades, the peptide fractions produced during cheese ripening have been more and more deeply described(HPLC, tandem mass spectrometry) even if their precise assessment remains challenging. As reviewed here, thisfraction is absolutely crucial in many cheese properties like flavor and/or texture, ecosystem regulation, and humanhealth via bioactive peptides. Actually, besides their well-known role in increasing bacterial growth rate, peptides areimplied in cell-cell communications between bacteria, in a positive (synergy) or negative (antimicrobial peptides) way.They also participate in building the casein network in the dairy matrices and are involved in their structural changesduring ripening, conferring various final textural properties like stretching. Finally, they are the most important sourcesof bioactive potentialities.However, the control of both the in situ release of peptides from caseins by proteinases, and their further hydrolysisby peptidases, is far from being achieved. Many proteinases, either from milk and coagulant agent or from bacterialorigins, are required to produce the first peptides in cheese. Plasmin and chymosin activities are well-studied, howevermany questions remain on the action of the bacterial proteinases. Moreover, the evolution of the peptide profile afterbacterial consumption during growth is only partially understood, in balance with the activity of intracellular peptidasesreleased through lysis.Actually, many bottlenecks exist. It is impossible to have a complete view of the peptides present in situ at each ripeningtime and to correlate this fraction with specific properties. It would require first the quantification of each peptideand second to take into account the interactions between them and the casein network. Lastly, very few are knownalso regarding their diffusion in dairy matrices. Peptidomics, metabolomics and new quantitative proteomic methods(iTRAQ) could be a future opportunity to bridge the gap between identification, quantification of peptides and certaincheese functionalities.