This study was conducted on female patients with different gynecological problems attending the gynecologyout-patient departments of two tertiary care hospitals in Peshawar city of Khyber Pakhtunkhwa, Pakistanbetween August 2012 and October 2013. The 200 patients had an age range of 21-65 years. Smears were takenwith cervical brushes and preserved in preservative medium and processed for manual liquid based cytology(MLBC) for Pap staining. Out of 200 collected samples, 30 samples were found inadequate on cytology. Of theremaining 170 samples, 164 (96.47%) were normal, 5 (2.94%) were of atypical squamous cells of unknownsignificance (ASCUS) and 1 (0.6%) was of high grade squamous intraepithelial lesion (HSIL). On PCR all thesamples were positive for beta globin gene fragment including those reported inadequate on cytology. Out ofthe 5 ASCUS samples, 2 samples were positive for HPV, one each for HPV 16 and HPV 18, and the rest of the 3samples were negative for HPV DNA. The 1 sample of HSIL was positive for HPV 16 on PCR. Out of 164 normalsamples on cytology, only 1 sample was HPV 16 positive. So overall, 4 (2%) out of 200 samples were positivefor HPV DNA, where 3 were HPV 16 (1.5%), and 1 was HPV 18 (0.5%) positive, and thus the ratio of infectionwith of HPV 16 to HPV 18 was 3:1 in the general population. In conclusion, PCR based HPV detection is a moresensitive method for screening of HPV infection than cytology as sample inadequacy does not affect the results.However, it can be combined with cytology methods in a HPV positive female to achieve the maximum results.