Dietary beans and peas provide fibre, resistant starch and other nutrients that are often lacking in the human diet. The influence of native starches of beans and peas (and microwaved preparations) on N utilisation, biochemical indices in blood serum and caecal ecosystem state (SCFA, bacterial enzymes, micro-organisms) was studied in vivo. The native pea starch contained more resistant starch compared with its bean counterpart (31 v. 17 %); however, processing decreased these amounts to 25 v. 10 %. N digestibility was found to decrease considerably in all experimental groups. A considerable reduction was observed in glucose and total cholesterol concentration in rat blood serum as a result of feeding both dietary legume starch preparations under microwave treatment. This indicates that starch of bean origin activated glycolytic bacterial enzymes; however, all the analysed starches were found to reduce the activity of β-glucuronidase. In addition, both dietary bean starches significantly induced the formation of SCFA in the caecal digesta. As compared with the control group, a significant decrease in the pH of caecal and colonic digesta was demonstrated for both bean starch preparations. In comparison with the diet with native pea starch, its microwaved preparation reduced the concentrations of acetic, butyric and propionic acids among caecal SCFA and increased the pH of caecal and colonic digesta. The atherogenic index was significantly lower in rats fed microwaved pea starch. All investigated starch preparations increased the population of Bifidobacterium spp. in caecal digesta, but were also good substrates for opportunistic Enterococcus or Escherichia coli.