Although urogenital infections with Chlamydia trachomatis are well recognized, less is known about infection at other body sites in adults. Pharyngeal specimens obtained from 706 heterosexual men and 686 women, and rectal specimens obtained from 1223 women who were at risk for chlamydia infection were cultured for C. trachomatis. Urogenital specimens were obtained from all patients. Chlamydia trachomatis was isolated from the pharynx in 3.7% of men and 3.2% of women. Recovery of chlamydiae was not associated with the presence of pharyngeal symptoms, but in women, but not men, it was associated with a history of oral-genital sex. The organism was also recovered from the rectum of 5.2% of the women. Rectal isolation did not correlate with a history of rectal symptoms or rectal sex but did correlate with concurrent genital infection. Infection at these sites may be important in the transmission or persistence of C. trachomatis infections.