OBJECTIVE To evaluate the efficacy of self-collected vaginal samples for high-risk HPV detection by the HPV oligonucleotide microarray method (HPVDNAChip). METHODS One hundred and eighteen patients with abnormal Pap smears were included. Self-collected vaginal and clinician-collected cervical samples for HPV testing were obtained. The result of the HPV DNA test was compared with the histopathological diagnosis or colposcopic finding. RESULTS Of the 118 patients, 42 (35.6%) had >or= cervical intraepithelial neoplasia (CIN) III lesions. Using the HPVDNAChip, high-risk types of HPV were detected in 38 of these 42 patients (90.5%) with the self-collected vaginal samples and in 37 of 42 (88.1%) with the clinician-collected cervical samples. The agreement of HPVDNAchip results between self- and clinician-collected samples was very good (kappa = 0.81) with a 93.2% concordance rate. Multiple HPV infections were found in 17 of 88 (19.3%) HPV-positive clinician-collected cervical samples. The rate of multiple HPV infection tended to decrease as the degree of pathologic classification increased. CONCLUSIONS Using the HPVDNAchip to assay for HPV infection, results from self-collected vaginal samples were compatible with those from clinician-collected cervical samples.