This study aimed to assess the performance of PCR as a means of detecting HPV 16/18 compared to the single probe-based PCR for detecting high-risk HPV, and evaluate these methods for detecting cervical intraepithelial neoplasia (CIN) in follow-ups for ASCUS testing. It also compares the costs of cytology, PCR methods, colposcopy and biopsy in the Brazilian Unified National Health System. Of the 81 patients with ASCUS, 41 (50.6%) tested positive for HPV 16/18 in PCR testing and 47 (58.02%) tested positive for high-risk HPV with single probe-based PCR testing. The negative predictive value was 93.75% for HPV 16/18 PCR and 100% for single probe-based PCR in cases that progressed to high-grade CIN. The annual costs of patient referral were the following: R$2,144.52 for referral of patients with ASCUS cytology for colposcopy; R$6,307.44 for referral of patients with ASCUS cytology and PCR positive for HPV 16/18 or colposcopy; R$3,691.80 for referral of patients with ASCUS cytology with single probe-based PCR positive for high-risk HPV. Therefore, cost per user can be reduced by performing single probe-based PCR for high-risk HPV on patients with ASCUS.