Human papillomavirus (HPV) infection frequently causes squamous intraepithelial lesions (SIL) of the uterine cervix and consequently gives rise to squamous cell carcinoma. It is therefore important to identify cases that potentially develop higher grades of SIL at an early stage of the disease. In this study, we thus investigated whether immunocytochemistry for p21(WAF1/Cip1) and p16(INK4a) could be applicable in the diagnosis and the prognostic prediction of SIL in combination with genomic analyses of HPV. The genomic analysis of high-risk HPV (hrHPV), which was done by reversed dot blotting and by in situ hybridization, and immunocytochemistry were performed on liquid-based cytological specimens. A cross-sectional study comprising 145 cases of NILM, ASC-US, LSIL, and HSIL indicated that the incidence of the positive cases for p16(INK4a) and p21(WAF1/Cip1) and hrHPV increased with the grade of SIL. A double positive status for p16(INK4a) and p21(WAF1/Cip1) was a significant discriminator between HSIL and LSIL/NILM, even when applied in conjunction with the genomic test for hrHPV (P = 0.006 by logistic regression analysis). However, a prospective study employing 61 NILM/ASC-US cases, revealed that the p16(INK4a) /p21(WAF1/Cip1) immunostaining was not a significant predictor for the progression of SIL, whereas the cytological diagnosis (NILM vs. ASC-US) and the infection status of hrHPV conferred significant effects on the prognosis. Immunostaining of p16(INK4a) and p21(WAF1/Cip1) provides additional information on the cytological diagnosis of SIL. A further analysis using a larger population is warranted to obtain a conclusive result regarding the prognostic significance of p16(INK4a) /p21(WAF1/Cip1) immunocytochemistry in the diagnosis of SIL.