The bacterial loads for gonococcal infections of the pharynx and rectum were determined among men with male sexual partners. The median bacterial load for rectal infections (18,960 copies/swab) was significantly higher than the load for pharyngeal infections (2,100 copies/swab; P = 0.001). Bacterial loads among men with symptomatic proctitis were strikingly high (median, 278,000 copies/swab).