The importance of legume proteins in cholesterol metabolism has been recognised, but the hindgut contribution is still unclear. The present work was undertaken to address the role of the caecum–colon in cholesterol metabolism in intact (I) and ileo-rectal anastomosed (IRA) pigs fed with casein or extruded soyabean (ES) diets. Four groups of six growing pigs were assigned to the treatments (casein–I, casein–IRA, ES–I, ES–IRA) for 3 weeks. Plasma total cholesterol, LDL- and HDL-cholesterol were not modified by surgery or diet. In the liver, the ES diet significantly depressed non-esterified, esterified and total cholesterol. The treatments did not affect hepatic 3-hydroxy-3-methylglutaryl CoA reductase, cholesterol 7α-hydroxylase or sterol 27-hydroxylase activities. In the gallbladder bile of ES-fed pigs, total cholesterol was depressed while total bile acid concentration was increased. IRA and the ES diet markedly decreased the biliary bile acid microbial metabolites (namely hyodeoxycholic acid) and increased the primary bile acids (mainly hyocholic acid). The concentration of bile hydrophobic acids was decreased only by the ES diet. Faecal neutral sterol output was increased in ES-fed pigs, but the bile acid and the sum of neutral and acidic steroid outputs were not. Microbial transformation of neutral and acidic steroids was markedly reduced by IRA, especially in the ES-fed pigs. Thus, surgery and ES modulated the steroid profile but the caecum–colon did not seem to play a crucial role in determining cholesterolaemia in pigs.