Detection of caprine arthritis-encephalitis virus (CAEV) infection in goats is currently limited to serologic testing or cell culture. We developed a polymerase chain reaction (PCR) assay to detect CAEV sequences in peripheral blood mononuclear cells (PBMC), synovial fluid cells (SFC), and milk cells (MC) obtained from infected goats. Results were positive for 18 of 20 PBMC, 8 of 8 MC, and 5 of 5 SFC samples from seropositive goats, whereas 3 of 33 PBMC samples and none of 8 MC or 5 SFC samples from seronegative goats were positive. Two of the PCR-positive and seronegative goats seroconverted upon follow-up testing 2 months later. This PCR assay provides a useful method for detecting CAEV infection in goats.