We have found cDNAs corresponding to a novel human P-glycoprotein gene in liver cDNA banks. The sequence of the 3' part of this cDNA reveals a domainal organization of the derived protein similar to that of the known P-glycoproteins and an 80% amino acid homology with the product of the human mdr1 gene (Chen et al., 1986). The new gene lies within 500 kb from mdr1 as determined by pulsed field gradient gel electrophoresis and is designated mdr3, as it appears to correspond to the third of the three P-glycoprotein genes mapped in the hamster multidrug resistance domain. mdr3 yields a transcript of 4100 nucleotides, 400 nucleotides less than the mdr1 transcript; the difference is accounted for by the shorter 3'-untranslated region of the mdr3 mRNA. Our cDNAs provide evidence for alternative splicing of mdr3 pre-mRNAs. One alternative is an insert of seven amino acids between the two major blocks of the nucleotide binding site and another is a deletion of 43 or 47 amino acids covering the putative transmembrane segment 5a. We speculate that these alternatives superimposed on differential expression of P-glycoprotein homologues could provide an explanation for the large variation in cross-resistance patterns observed in cell lines selected for multidrug resistance with different cytostatic drugs.