Hamartomatous gastrointestinal polyposis syndromes have always been considered as non-neoplastic. Nevertheless, an increased cancer risk both within and outside the gastrointestinal tract may exist in these syndromes. The hamartomatous polyps may sometimes harbor dysplasia, but their neoplastic potential is unknown. The genetic defects causing the hamartomatous syndromes are less well established than, for example, familial adenomatous polyposis (FAP) and hereditary non-polyposis colorectal cancer (HNPCC). The genetic studies on the Mendelian inherited syndromes FAP and HNPCC have made a major contribution to the identification of genes involved in colorectal tumorigenesis. The genes involved in colorectal cancer development may also contribute to cancer development in the hamartomatous polyposis syndromes, and are currently under investigation. Furthermore, new insights into the development of various cancers may be obtained by the isolation and characterization of genes involved in Mendelian inherited hamartomatous polyposis syndromes. This report summarizes the available literature on this subject, and describes the pheno- and genotypic features of the hamartomatous syndromes of juvenile polyposis, Peutz-Jeghers syndrome, and Cowden's disease.