The peplomer gene of feline infectious peritonitis virus (FIPV) strain 79-1146 was isolated from a genomic cDNA library by differential hybridization with RNA 2 and 3 as probes. From the nucleotide sequence a primary translation product of 1452 residues (Mr 160,472) was predicted, containing an N-terminal signal sequence, a C-terminal transmembrane segment and 35 potential N-linked glycosylation sites. By S1 nuclease analysis the 5' end of the presumptive RNA 2 body was located at about 30 nucleotides upstream from the initiating AUG codon. At approximately the same position a nine nucleotide sequence ACUAAACUU was found, which was also present 37 nucleotides downstream from the open reading frame. Comparison of the sequences of the FIPV, murine hepatitis virus and infectious bronchitis virus peplomer proteins showed about 27% overall homology, with most conservation in the C-terminal half.