Prevalence and site-pathogen studies of pathogenic Neisseria were conducted in 815 homosexual men over a 12-month period. Neisseria meningitidis was isolated from more patients than N gonorrhoeae (43.1% vs 33.1%). A high oropharyngeal carriage of n meningitidis (42.5%) was present, with much lower urethral (0.7%) and rectal (2.0%) colonization. Although N meningitidis urethral isolates were associated with urethral discharge in five of six patients, N meningitidis in the oropharynx or rectum was not usually associated with clinical illness. Neisseria meningitidis was usually isolated from only one site in individual patients. Neisseria gonorrhoeae was isolated from the urethra (18.5%), rectum (16.3%), and oropharynx (5.6%). Of the 270 patients with gonococcal infection, 49.1% had urethral gonorrhea only, and 20.7% were infected at two or more body sites. Virtually all patients with urethral infection had symptoms of urethritis, whereas 89.1% of patients with oropharyngeal infection and 61.9% of patients with anorectal infection had no local symptoms.