HIV-RNA testing may identify individuals with primary HIV infection. Men who have sex with men (MSM) having HIV testing through Public Health, Seattle and King County were screened for primary infection through pooled RNA testing. Eighty-one out of 3525 specimens (2.3%) had detectable antibody and RNA, and seven out of 3439 antibody-negative specimens (0.2%) had HIV RNA. Targeted screening for primary infection through pooled RNA testing in MSM is a useful addition to HIV case finding.