Three human squamous carcinoma cell lines (FaDu, A253, and SQCC/Y1) were tested for sensitivity to methotrexate (MTX) and trimetrexate, a second generation folate antagonist in clinical trials. Two of the three cell lines (A253 and SQCC/Y1) showed inherent resistance to methotrexate, when cytotoxicity was evaluated after short term exposure (4 and 24 h). In contrast, all three cell lines were markedly sensitive to trimetrexate, an antifolate which is taken up by cells by a different transport system than is methotrexate and which is not polyglutamylated. The basis for the natural resistance to methotrexate shown by two of the three cell lines was examined. Levels of dihydrofolate reductase activity, inhibition of this enzyme by methotrexate, and influx of MTX did not differ significantly between the three cell lines; however, resistance was correlated to the amounts of polyglutamates of methotrexate synthesized by the three cell lines. After a 24-h incubation with 10 microM MTX, the A253 cell line was able to form only 35.0 pmol/10(7) cells of polyglutamates, compared to 250 pmol/10(7) cells synthesized by the FaDu cell line, while the SQCC/Y1 cell line, intermediate in sensitivity to methotrexate, was able to form 145 pmol/10(7) cells of MTX polyglutamates. The A253 cell line contained less folylpolyglutamate synthetase activity compared to the FaDu and SQCC/Y1 cell lines. However, it is not clear if this difference is sufficient to explain the marked differences in polyglutamates of methotrexate found between the cell lines. We conclude that decreased polyglutamylation of methotrexate in some human squamous cell carcinomas may be the major contributing factor in inherent resistance to high dose pulse administration of this drug.