O6-Methylguanine-DNA methyltransferase (MGMT) plays an important role in protecting cells from the mutagenic potency of alkylating agents. This study addresses the role of DNA methylation in the expression of the human MGMT gene. Southern blot analysis of DNA from human Mer+ (MGMT proficient) and Mer- (MGMT deficient) cell lines demonstrated that the methylation state of a unique SmaI site in the MGMT gene promoter, previously shown by others to be invariably unmethylated in Mer+ cells and methylated in Mer- cells, did not correlate with the Mer phenotype. Neither was there any significant difference in the density of CpG methylation in the MGMT gene 5'-flanking sequences between Mer+ and Mer- cells. On the other hand, the body of the MGMT gene was less methylated in most Mer- cells relative to Mer+ cells, and in three of six Mer- cell lines the gene was essentially methylation-free. Interestingly, the Mer- cells that were hypomethylated in the MGMT gene also tended to be less methylated at other loci. Widespread hypomethylation is a frequent trait in carcinogenesis, and may be involved in development of the frequently found Mer- phenotype.