Previous studies have shown that DNA topoisomerase II enzyme activity and protein levels are reduced in cloned lines of Adriamycin-resistant P388 leukemia cells relative to drug-sensitive cells (Deffie et al., Cancer Res., 49: 58-62, 1989). The molecular basis of the reduced topoisomerase II levels in these resistant cells has been investigated. Northern blot analysis of total cellular RNA from drug-sensitive and -resistant cells using a 1.8-kilobase human topoisomerase II complementary DNA revealed the presence of two mRNA species: a 6.6-kilobase transcript that was strongly expressed in drug-sensitive cells but reduced 7- to 8-fold in resistant cells; and a 5.5-kilobase transcript detected only in drug-resistant cells. Southern blot analysis of genomic DNA digested with BamHI, StuI, or PvuII and probed with the 1.8-kilobase complementary DNA for human topoisomerase II showed that, in Adriamycin-resistant cells, there were two different alleles for topoisomerase II, one identical to the native allele but with a lower gene copy number than that found in sensitive cells, and a second allele containing a mutation present only in resistant cells. These findings suggest that the reduced levels of topo II protein in drug-resistant cells may be due to reduced amounts of the native 6.6-kilobase mRNA. The unique 5.5-kilobase mRNA in resistant cells may represent a shortened transcript of the mutated topoisomerase II allele.