Human papillomavirus (HPV) is the principle cause of cervical carcinoma (CC). Detection and screening programs for this malignancy is formerly based on cytological examination of cervical cells. However, the recent trend is for detection of HPV DNA in cervical swabs (CSs). In either cases, the collection of specimens require pelvic examination which is unfavorable for women and time consuming for healthcare providers. Using urine sample for HPV DNA detection is a very good alternative; however, the efficiency of such samples in this regard is questionable. This cross-sectional study aimed to evaluated the efficiency of urine samples in detection of HPV DNA compared with CSs, and to determine the genetic relatedness of local HPV isolates from urine and CSs through phylogenetic analysis. Pair samples of first voided urine and CSs were collected from a total of 100 married women with child bearing age suffering from vaginal discharge. Cervical swabs were kept at -20°C until be used, while urine samples were processed at the same day of collection. From both specimens, viral DNA was extracted and two sets of universal primers were used to amplify L1 capsid gene in a nested-PCR, the products of which were subjected for direct sequencing. The resultant sequences were aligned with reference sequences in Gen Bank. MEGA 6 software was used to construct the phylogenetic tree from local isolates and 19 reference sequences.  HPV DNA was detected in 13% and 10% of CSs and urine samples respectively. Phylogenetic analysis for local HPV isolates from cervical samples revealed that 8 (61.54%) isolates were low risk (LR) HPV. The other five isolates were high risk (HR) HPV. Kappa statistic revealed 0.853 concordance between urine samples and CSs in HPV DNA detection (95% confidence interval (CI)=0.0.696–1.01, P<0.001), with 96.7% sensitivity and 100% specificity. These data strongly indicated the efficiency of urine sample in HPV detection with excellent sensitivity and specificity. Thus, urine samples could be used for routine detection and screening for HPV infection in women with child-bearing age.