The lentivirus caprine arthritis-encephalitis virus (CAEV) is closely related by nucleotide sequence homology to visna virus and other sheep lentiviruses and shows less similarity to the other animal and human lentiviruses. The genomic organization of CAEV is very similar to that of visna virus and the South African ovine maedi visna virus (SA-OMVV) as well as to those of other primate lentiviruses. The CAEV genome includes the small open reading frames (ORF) between pol and env which are the hallmarks of the lentivirus genomes. The most striking difference in the organization of CAEV is in the env gene. The Env polyproteins of visna virus and the related SA-OMVV contain 20 amino acids between the translational start and the signal peptide not present in CAEV. In addition to nucleotide sequence analysis, the transcriptional products of CAEV were determined by Northern analysis. The viral mRNA present in cells transfected with the infectious clone reveal a pattern characteristic of the mRNAs observed in other lentivirus infections. The putative tat ORF of CAEV could be identified by genomic location and amino acid homology to the visna virus tat gene. However, the CAEV rev gene could not be identified in a similar fashion. Thus, to determine the location of the rev ORF cDNA clones were obtained by PCR amplification of the mRNA from infected cells. To determine if a Rev response element was contained in the CAEV genome, secondary structural analysis of the viral RNA was performed. A stable stem loop structure which is similar in location, stability, and configuration to that determined for the Rev response element of HIV was found.