Genotoxic tolerance to low-level exposure of monofunctional alkylating agents is compound specific, with the mechanism pertaining to alkyl-induced genotoxic threshold response as yet unknown. N-methylpurine DNA glycosylase (MPG), an initiator glycosylase of the base excision repair (BER) pathway, typically repairs alkyl-induced DNA adducts, many of which are associated with genomic instability and tumorigenic risk. Here we demonstrate the involvement of MPG in modulating the genotoxic threshold response induced by the Sn2 alkylating agent ethyl methanesulfonate (EMS) and not the Sn1 alkylating agent N-ethyl-N-nitrosourea (ENU) in human lymphoblastoid cells and suggest the lack of N7-ethylguanine adduct repair as a key factor attributable to an observed increase in EMS-induced chromosome damage. Moreover, an increase in MPG messenger RNA expression levels in response to EMS and not ENU doses administered below the low-observed effect level substantiates the proposed specific involvement of MPG in relation to EMS-induced genotoxicity. We further report an unexpected dose-dependent decrease in the mutation frequency of the MPG-deficient cell line M09B when challenged with ENU, a response deemed consequential to a pronounced dose-dependent increase in the number of apoptotic cells relative to wild type. Collectively, these findings implicate the differential involvement of MPG-directed BER as a primary mechanism of action for the chromosome damage threshold response and cytotoxicity induced by alkane sulfonates and N-nitrosourea compounds, respectively.