A cDNA clone encoding the full coding region of polymorphic arylamine N-acetyltransferase was isolated from rabbit liver and expressed in Chinese hamster ovary cells. The expressed enzyme acetylated 2-aminofluorene, procainamide, sulfamethazine, and p-aminobenzoic acid at equivalent rates. N-Acetyltransferase activity was measured in 17 rabbits from an inbred colony which were classified into rapid, intermediate, and slow acetylators. The livers of the rapid and intermediate acetylators efficiently acetylated all four substrates, while the liver from the slow acetylator showed a low but significant activity with p-aminobenzoic acid. Immunoblot and Northern blot analyses of rabbit livers indicated that the differences in N-acetyltransferase activity were due to differences in N-acetyltransferase protein and mRNA content. Genomic clones of N-acetyltransferase were isolated from the rapid and slow acetylator rabbits. The nucleotide sequence of the gene from rapid acetylator rabbit was identical to that of the cDNA, while the sequence of the gene from slow acetylator rabbit was homologous, but not identical, to the cDNA sequence. Genomic Southern blot and polymerase chain reaction analyses of the genomic DNAs and cDNAs from the three types of acetylator indicated that the gene for polymorphic arylamine N-acetyltransferase is totally deleted in the slow acetylator rabbit, while the gene from slow acetylator rabbit is expressed in all rabbits and might encode another N-acetyltransferase. Thus the genetic mechanism of N-acetyltransferase polymorphism in rabbit liver is essentially different from that of human liver as demonstrated in this laboratory (Ohsako, S., and Deguchi, T. (1990) J. Biol. Chem. 265, 4630-4634; Deguchi, T., Mashimo, M., and Suzuki, T. (1990) J. Biol. Chem. 265, 12757-12760).