Digestion and absorption of lipids is a highly efficient process. From Western diets about 95% will be absorbed. This implies that together with lipids from endogenous sources 6-8 g of lipids will enter the colon daily. This input significantly increases during various lipid malabsorption syndromes. It has long been assumed that the biological fate of unabsorbed lipids is physiologically not relevant. However, significant microbial lipid metabolism occurs. Circumstantial evidence is arising which supports a role of unabsorbed lipid metabolites in the development of colonic diseases. Lipid metabolites may act as detergents in the colon, leading to mucosal injury and reactive hyperproliferation, which in its turn could promote tumour development. Lipid metabolites could also be transformed in biological active metabolites, which have a tumour promoting potency. More mechanistic information is needed on the colonic metabolic fate of lipids in order to develop strategies for manipulating colonic flora in the prevention of lipid related colonic diseases.