This study aimed at identifyingmilk peptides released in the gastrointestinal tract ofmini-pigs during the digestion of dairy matrices and determining the effect of the matrix structure on the gut lumen peptidome. Six dairy matrices (raw and heated milk, the corresponding rennet gels, and a non-stirred or a stirred acid gel prepared from the heated milk) of similar composition but with different structures were ingested by four mini-pigs. Duodenal effluentswere collected over a 5 h-period and analyzed by tandemmass-spectrometry.More than 16,000 peptideswere sequenced and unambiguously identified. The structure of dairy products had only little influence on the location of cleavage sites on the protein sequences.However, it strongly impacted the number of identified peptides andmore especially for rennet gels which led to about 3 times less detected peptides than for the other matrices. This effect was attributed to greater extents of dilution by digestive secretions associated with longer gastric retentions for the rennet gels. Potential bioactive peptides were also produced over time and are all reported to contribute to document the literature originating from in vivo experiments. Our results indicate that the structure of dairymatrices strongly affects the kinetics ofmilk protein digestion in vivo, more than themechanism of proteolysis itself.