Various alterations of the dihydrofolate reductase (DHFR) gene are involved in resistance. In order to understand the mechanism that induce such gene alterations in human leukemia cells, we studied the expression products of DHFR gene in trimetrexate (TMQ)- and/or methotrexate (MTX)-resistant sublines derived from a MOLT-3 human leukemia cell line. A 200-fold TMQ-resistant subline (MOLT-3/TMQ200) expressed the mutated DHFR mRNA, with a base change (T-->C) at the second position of codon 31, as well as the wild type gene. A MTX-resistant subline derived from MOLT-3/TMQ200 (MOLT-3/TMQ200-MTX500) showed a further increase in the expression of the mutated DHFR mRNA, compared to MOLT-3/TMQ200, with a marked decrease of expression of the wild type DHFR mRNA, which is confirmation of amplification of the mutated DHFR gene. By contrast, a 10,000-fold MTX-resistant subline (MOLT-3/MTX10,000) over-expressed the wild type DHFR mRNA, which is confirmation of amplification of the wild type gene. Increased levels of the DHFR enzyme in these sublines were proportional to expression levels of the DHFR mRNA. The DHFR enzyme expressed in MOLT-3/TMQ200-MTX500 cells showed a 40-fold increase in the Ki values for both MTX and TMQ, compared with values for the wild type DHFR expressed in both MOLT-3/MTX10,000 and its parent cell line. These findings suggest that the altered DHFR gene, which was introduced in MOLT-3 cells by exposure to TMQ, gave rise to a variant enzyme with reduced affinity to antifolates, and that complex DHFR alterations confer drug-resistant phenotypes in antifolate-resistance. Structural difference between the antifolates could be important in the introduction of the differential DHFR gene alterations in the antifolate resistance.