Microsatellite instability (the replication error phenotype) is a new molecular assay that identifies a substantial fraction of human cancers. The microsatellite instability in these cancers arises from alterations in the tumors of the number of mono-, di-, and trinucleotide repeats that compose the microsatellites. Microsatellite instability is typical of colon and endometrial tumors arising in members of Lynch syndrome cancer families. Microsatellite instability is also found in a substantial percentage of sporadic cases of colon, endometrial, and gastric cancer, as well as in additional sporadic cancers, such as lung cancer, not usually seen in Lynch kindreds. Thus far, four different mutant genes, all homologous to bacterial DNA repair genes, have been identified as inherited in Lynch kindreds, and therefore are associated with the replication error phenotype. Clinical implications of the replication error phenotype include the demonstration that resistance to some alkylating agents appears to be directly altered in tumors with this phenotype.