The human gastro-intestinal tract hosts a complex and diverse microbial community, whose microbiome encodes biochemical pathways that humans have not evolved. As a consequence, the gut microbiota produces metabolites from a large range of molecules that host’s enzymes are not able to convert. This is of first importance as these bacterial metabolites may have beneficial or deleterious effects on human health. In particular, cholesterol and bile acids are exposed to the gut microbiota and undergo bacterial metabolism: cholesterol is mainly converted into coprostanol, a non absorbable sterol which is excreted in the feces. Conversely, over twenty different secondary bile acid metabolites are produced by the gut microbiota from the primary bile acids: cholic and chenodeoxycholic acids. The main bile salt conversions in the human gut include deconjugation, oxidation and epimerization of hydroxyl groups at C3, C7 and C12, 7-dehydroxylation, esterification and desulfatation.