The study aimed to investigate the in vivo digestion of Phaseolus vulgaris phaseolin types differing in their subunit pattern composition. Diets contained either casein as the sole source of protein or a mixture (1:1) of casein and pure Sanilac (S), Tendergreen (T) or Inca (I) phaseolin either unheated or heated. Rats were fed for 11 d with the experimental diets. Their ileal content and mucosa were collected and prepared for electrophoresis, Western blotting, densitometry and MS. Differences in digestion among native phaseolin types were observed for intact phaseolin at molecular weights (MW) of 47–50·5 kDa and for an undigested fragment at MW of 19–21·5 kDa in ileal digesta. In both cases, the concentration of these protein bands was lower for I phaseolin than for S or T phaseolin (P < 0·05). In the mucosa, the concentration of a protein band at MW of 20·5–21·5 kDa was lower for S phaseolin as compared to T or I phaseolin (P < 0·001). The presence of phaseolin subunits and their fragments was confirmed by Western blotting. MS analysis revealed the presence of undigested α and β subunit fragments from phaseolin and endogenous proteins (anionic trypsin I and pancreatic α-amylase) in ileal digesta. Thermal treatment improved digestion (P < 0·01), acting on both dietary and endogenous protein components. In conclusion, this study provides evidence for differences in intestinal digestion among phaseolin types, S phaseolin being more resistant and I phaseolin more susceptible. These differences were affected by the origin of the phaseolin subunit precursor. Heat treatment enhanced phaseolin digestion.