Abstract: Present study is aimed at comparison between cytological method and polymerase chain reaction in the diagnosis of HPV infection among patients with cervical cancer. Cervical cancer is one of the common reproductive system cancers in developing countries that involve a much numbers of women annually. It is believed that human papillomavirus protein products including E6 and E7 cause transformation. Forty five women out of 166 studied ones were infected by HPV (p = 0.1). Among these 45 patients, 24 cases were recognized with HPV 16 (p = 0.2), 14 with HPV 18, 3 with both HPV 16 and HPV 18 and 4 with other types of HPV. PCR indicated 31 samples with HPV infection (24.03%) whereas cytology could only find 4 HPV infected patients (3.11%). The difference was statistically significant (p = 0.003). We conclude that PCR is more sensitive to diagnose HPV infection and also its type than cytology.