Objective:To detect the human papillomavirus by two methods in a sample of Iraqi women complaining of multiple gynecological symptoms and to verify the most accurate way for detection of such virus. Design :A prospective study including a total number of symptomatic cases obtained from patients referred to the Iraqi National Cancer Research Center, the period from Sep.2011 to Dec. 2012 for clinical or colposcopic suspicion of HPV infection. Setting:Al-Yarmouk Teaching Hospital& Iraqi National Cancer Research Center. Population:One hundred women who suffered from different gynecological problems were subjected to Pap smear. Method:The data collected from the patients referred to the Iraqi National Cancer Research Center, Pap smear and HPV testing by PCR were done for all patients, but the colposcopy directed biopsy was done only for 45 cases which gave abnormal Pap smear results and screening of virus by immune histochemical assay. Results:The overall prevalence of PCR sensitivity for detection of HPV, in this study there was only one case of HPV positive result detected by PCR in contrast to 10 cases of positivity detected by immune histochemical, and the most positive cases were within the low–grade intraepithelial lesion. Conclusion:Our study showed the detection of HR HPV infection detected by cervical cytology is susceptible to errors. Both methods of detection of HPV (PCR and immune histochemical assay) are complex laboratory measures requiring numerous processes by humans and machines.Our study showed that histoimmune detection of HPV was higher in number compared to the PCR detection of HPV.Our results of Pap smear and colposcopy-directed biopsy were strongly comparable.We know that the PCR has higher sensitivity in detection of HPV infection,so this result need to be assessed thoroughly about the accuracy of such method in our country.