This study aimed at identifying milk peptides released in the gastrointestinal tract of mini-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 effluents were collected overa 5h-period and analyzed by tandem mass-spectrometry. More than 16,000 peptides were 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 and more 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 dairy matrices strongly affects the kinetics of milk protein digestion in vivo, more than theme chanism of proteolysis itself.