The high incidence of invasive cervical cancer among those who have not undergone cancer screening is a serious problem. This study aimed to investigate the utility of human papillomavirus (HPV) test results from self-collected urine and vaginal samples as screening tools. The study was conducted in two steps. First, the appropriate storage container, temperature, and time until urine HPV assay performance were verified. Second, the results of spot urine testing under those conditions and of gynecologist-collected cervical and self-collected vaginal samples were compared to verify the feasibility of using the BD Onclarity® HPV assay for individuals with abnormal cervical cytology. The participants were 121 women with abnormal cervical cytology. Self-collected urine and vaginal samples, along with gynecologist-collected cervical samples, were tested for HPV using the BD Onclarity® HPV assay. The optimal conditions for urine sample storage were identified by comparing the HPV detection rates under various conditions. Urine stored in a BD Probe Tec™ (QxUPT) for less than 72 h at room temperature was found to have the highest HPV positivity rate. Under these conditions, the detection rates of HPV in urine, cervical, and vaginal samples were examined. HPV type 16 was detected in 41.7% of the cervical samples, type 18 in 10%, and types 31 and 52 in 12.6% each. The concordance rate for HPV testing between clinician-collected cervical and urine samples was 63.9% (kappa: 0.34; 95% CI: 0.21-0.47), and that between clinician-collected cervical and self-collected vaginal samples was 77.8% (kappa: 0.68; 95% CI: 0.53-0.83), indicating good concordance. In a population with an HPV-related lesion/tumor prevalence of approximately 70%, the sensitivity of HPV testing was 82.7% for the cervix, 46.4% for urine, and 75.7% for vaginal samples. The primary limitation is the lower detection rate of HPV in spot urine samples than in other sample types, indicating room for methodological improvement. The study's findings are based on a specific population, which may limit generalizability. We investigated the optimal self-collected urine-to-testing time and temperature. Self-collected vaginal and urine HPV tests show moderate-high concordance with clinician-collected cervical HPV tests, suggesting their potential utility for women who do not undergo regular cancer screening. However, the sensitivity was not high in spot urine. Therefore, further large-scale studies are needed to verify these findings and optimize testing methods to encourage broader participation in cancer screening programs.