Chlamydia trachomatis and HPV coinfections in the male population are often a disregarded issue. We performed a study to evaluate the prevalence of such infections in heterosexual HIV negative men from a Northern Italy multi-ethnic area at high prevalence for cervical malignancies. Urethral swabs (US) or first-voided urine were evaluated retrospectively from 1317 patients attending Sexually Transmitted Infections (STI) clinic and from 3388 outpatients attending private clinics. Informations about participants' demographic characteristics and attributes of C. trachomatis, including chronic infection, and HPV genotypes testing, were collected. Exact Fisher test, bivariate, and multivariate logistic regressions were carried out. The prevalence of C. trachomatis was 1.7% in the outpatients and 16.9% in the STI group (P < 0.0001) in which the highest frequency was observed in men of age ≤25 years. Among patients with C. trachomatis, asymptomatic HPV co-infection was detected in 33% of men from the STI clinic and in 2% of the outpatients. Out of all coinfections, 56% were due to single HPV, with a prevalence of 73% in young STI men. The distribution of HPV genotypes confirmed the increased circulation of LR-HPV42, HR-HPV51, HR-HPV52 and prHR-HPV82, and the decreasing of HR-HPV16. African nationalities and leucorrhea were significantly associated risk factors, while the regular condom use offered an effective protection. This study highlights the high prevalence of C. trachomatis and HPV asymptomatic co-infection in young HIV negative men attending the STI clinic, representing a reservoir of new HPV genotypes with potential oncogenic risk.