The prevalence of Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) in 232 sexual assault victims who presented for examinations between August 1, 1987, and July 31, 1988, was determined. Results are reported for cervical, rectal, and oropharyngeal NG cultures and for cervical and rectal CT smears. Results from a one-week follow-up are also reported. Cervical test results from the initial sexual assault examination were compared with cervical tests on 399 randomly selected female emergency department patients who presented for other gynecological conditions or lower abdominal pain. The victims of sexual assault had ten of 210 positive cervical NG cultures (4.76%), and 13 of 213 positive cervical CT smears (6.1%) at the first visit. These prevalence rates were not significantly different (P = .3058). There were none of 28 positive rectal NG cultures (0%) and one of 22 positive rectal CT smears (4.34%) (P = .451). None of the 43 oral NG cultures was positive. Seventy-three victims returned for follow-up examination. No follow-up cervical, rectal, or oral NG cultures were positive. However, one of 53 follow-up cervical smears for CT was positive, but this was not significantly different than for cervical NG (P = .461). Sexually assaulted patients had ten of 210 (4.76%) cervical NG cultures positive, and nonassaulted patients showed 53 of 393 positives (13.4%) (P less than .001). Assaulted patients had 13 of 213 (6.1%) cervical CT smears positive, and nonassaulted patients showed 33 of 352 (9.3%) positives (P = .11).(ABSTRACT TRUNCATED AT 250 WORDS)