Analysis of male HPV infection is hindered frequently by the lack of consistency in collection methods and sample adequacy for detection of HPV with molecular methods. Presented here are the reliability of sample collection of male anogenital skin exfoliated cells, as well as reliability of PCR-based HPV detection method and genotyping analysis. Concordance of HPV test for paired collected samples from different anatomical sites was determined. The highest agreement was observed for penile shaft with a kappa (kappa)=0.75 (95% CI: 0.63-0.86), followed by perianal area (kappa=0.68, 95% CI: 0.51-0.86); and lowest at the anal canal (kappa=0.55, 95% CI: 0.35-0.74) and scrotum (kappa=0.54, 95% CI: 0.40-0.69). The reliability of laboratory testing was highest for detection of oncogenic types (kappa=0.86, 95% CI: 0.71-1.00) and for multiple-type HPV infections (kappa=0.84, 95% CI: 0.72-0.95) compared to detection of non-oncogenic HPV types (kappa=0.64, 95% CI: 0.47-0.82) or single HPV-type detection (kappa=0.52, 95% CI: 0.32-0.72). In conclusion, the swab method used to obtain skin exfoliated cells is adequate for sample collection, and the specimens can be used reliably for molecular HPV testing.