To evaluate methods for detection of genital human papillomavirus (HPV) DNA in men, samples were obtained from 3 consecutive groups of 10 men attending a sexually transmitted disease clinic by use of (1) a saline-wetted Dacron swab alone, (2) a saline-wetted cytobrush, or (3) emery paper (600A-grit Wetordry Tri-M-ite; 3M) abrasion followed by a saline-wetted Dacron swab. By use of a polymerase chain reaction-based assay, 45% of emery-paper samples were found to be positive for beta-globin, compared with 23% of swab-alone and 0% of cytobrush samples. Subsequently, emery paper and saline-wetted Dacron swabs were used to obtain penile shaft, glans, foreskin, and scrotum samples from 318 male university students. Urine samples were also obtained. Of 1323 samples tested, 1288 (97%) were found to be positive for beta-globin. HPV DNA was detected in samples from 104 men (33%): 24% from the penile shaft, 16% from the glans, 28% from the foreskin, 17% from the scrotum, and 6% in urine. The HPV prevalence was similar for circumcised and uncircumcised men. Testing multiple sites increased the number of men for whom HPV DNA was detected.