Methotrexate (MTX) covalently linked to poly(L-lysine) [poly(Lys)] enters cells by endocytosis, is degraded in lysosomes and, upon liberation of small molecular methotrexate, is cytocidal to Chinese hamster cells in culture. This drug conjugate was used to select mutants resistant to MTX-poly(Lys), which were examined for defects in endocytosis. Two mutants resistant to MYX-poly(Lys) and sensitive to free MTX, MPL 3-4 and MPL 2-5, internalized the conjugate in normal fashion, but had a decreased ability to degrade it to small molecular drug. The magnitude of this defect in the two mutants correlated with their level of resistance. In addition, both mutants were cross resistant to diphtheria toxin and modeccin and hypersensitive to ricin. While MPL 3-4 internalized MTX-poly(Lys) and inulin normally, it showed decreased endocytosis via the mannose-6-phosphate receptor and decreased uptake of 125I-alpha-2 macroglobulin. Acidification of subcellular fractions was measured using the partitioning of acridine orange. In MPL 3-4, the ATP-driven acidification of the endosome-containing cell fractions was slightly decreased (80% of controls), while acidification of the heavy lysosome-containing fraction was normal. Complementation analysis using hybrids of MPL 3-4 x MPL 2-5 indicated that the mutations occurred at the same gene, but were expressed with different severity. This genotype is identical to that of the End 2 mutants described by Roff et al. (1986). Thus, surprisingly, mutants with identical genotypes were isolated independently by totally different selection procedures.