Although drug therapy is critical for control of amoebiasis, little is known about mechanisms of drug resistance by E. histolytica parasites. Here we tested the hypothesis that multidrug resistant (mdr) amoeba mutants, similar to mdr tumor cells, are drug resistant based upon overexpression of a P-glycoprotein pump that effluxes drugs from the cells. Using primers to conserved regions of the human P-glycoprotein and the polymerase chain reaction (PCR), we identified multiple 344 base par segments of amoeba DNA similar to the mammalian P glycoprotein. The amino acid sequences of amoeba mdr-like PCR products were from 53 to 97 identical with each other, 55 to identical to human mdr1 sequences, and 41-44% identical with P. falciparum mdr-like sequences. On northern blots, the mdr-like PCR products identified amoeba mRNAs 4.5-5 kilobases long, similar to the 5 kilobase mRNAs reported for the mammalian mdr gene. These mRNAs were increased at least seven times in emetine resistant mutant clone C2 amoebae versus wild-type clone A parasites. Further, the expression of the mdr-like mRNAs was increased three to four times when clone C2 mutants were grown under drug pressure versus the same parasites grown without emetine. In contrast, the number of genomic copies of the mdr-like DNA segments was not increased in the mutant clone C2 versus the wild-type clone A amoebae, and no rearrangements of the mdr-like DNA segments by the mutant were identified on Southern blots. In conclusion there appears to be a family of mdr-like genes in E. histolytica, which may be involved in drug resistance by the parasite.