Lynch syndrome, one of the most common cancer susceptibility syndromes, is caused by germline mutations of genes affecting the mismatch repair proteins MLH1, MSH2, MSH6 or PMS2. Most of these mutations disrupt the open reading frame of the genes involved and, as such, lead to constitutive inactivation of the mutated allele. In a subset of Lynch syndrome patients MSH2 was found to be specifically inactivated in cell lineages exhibiting EPCAM expression. These patients carry deletions of the 3′ end of the EPCAM gene, including its polyadenylation signal. Due to concomitant transcriptional read-through of EPCAM, the promoter of MSH2 15 kb further downstream becomes inactivated through hypermethylation. As these 3′ EPCAM deletions occur in the germline, this MSH2 promoter methylation ('epimutation') is heritable. Worldwide, numerous EPCAM 3′ end deletions that differ in size and location have been detected. The risk of colorectal cancer in carriers of such EPCAM deletions is comparable to that of MSH2 mutation carriers, and is in accordance with a high expression of EPCAM in colorectal cancer stem cells. The risk of endometrial cancer in the entire group of EPCAM deletion carriers is significantly lower than that in MSH2 mutation carriers, but the actual risk appears to be dependent on the size and location of the EPCAM deletion. These observations may have important implications for the surveillance of EPCAM deletion carriers and, thus, calls for an in-depth assessment of clinically relevant genotype-phenotype correlations and its underlying molecular mechanism(s). © 2013 Springer Science+Business Media Dordrecht.