Background: Human papillomavirus (HPV) is a very common sexually transmitted disease affecting both men and women and is responsible for different ano-genital cancers in either sex. Co-existing sexually transmitted infections (STI) including HIV have been considered as important co-factors for carcinogenesis induced by HPV. The purpose of this study was to determine the prevalence of any HPV, HPV 16 and HPV 18 and also concomitant STIs among female sex workers (FSW), men having sex with men (MSM) and injectable drug users (IDU). Material and Method: This cross-sectional study was conducted among 45 FSWs, 26 MSMs and 58 IDUs who attended the STI or de-addiction clinics. Genital scrape samples collected from glans penis and coronal sulcus in males and cervical squamo-columnar junction in females were tested for HPV DNA by PCR using HPV L1 consensus primer. Type specific PCR to detect HPV 16 and 18 was done on the samples positive on consensus PCR. All participants were tested for associated STIs including HIV and hepatitis B and cervical cytology was done on all females. Results: Among the FSWs, HPV was detected in 73.3% and HPV 16 and 18 was detected in 25.7%. Though the HPV prevalence was similarly high among MSMs (69.2%) and IDUs (72.4%), the prevalence of HPV 16 and 18 was much lower in these groups compared to the FSWs. Prevalence of cervico-vaginal infection with Trichomonas vaginalis and syphilis was significantly higher in the HPV positive women compared to the HPV negative women. There was no statistically significant difference in the prevalence of other STIs among HPV positive and negative women and men. Conclusion: HPV infection is highly prevalent among FSW, MSM and IDUs. Trichomonas vaginalis infection is more frequent in HPV positive women.