The intestinal microflora are capable of performing a wide variety of metabolic transformations. The digestive tract can be exposed to orally ingested, bile excreted, or blood-borne exogenous and endogenous substances that can be converted by the intestinal flora into carcinogens, mutagens, cocarcinogens or tumor promoting agents. In addition, the intestinal microflora can metabolize a wide variety of pharmacological agents resulting in production of metabolites required for the physiological activity of these agents or conversely in the inactivation of these agents. This article reviews the current knowledge of the relationship between the intestinal microflora and the metabolic reactions leading to the transformation of drugs and the production of mutagenic or carcinogenic compounds. The composition and distribution of bacteria in the gastrointestinal tract is discussed and the type of reactions these bacteria perform is summarized. The conversion of specific substrates such as, rutin, digoxin, cycasin, azulfidine and cyclamate are discussed and the physiological implication of these conversions are presented.