Background: Sexually transmitted infections (STIs) affect sexual and reproductive health of millions of men. Pathogens such as human papillomavirus (HPV), herpes simplex virus type 1 and 2 (HSV-1 y HSV-2), Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis and Ureaplasma urealyticum are associated with STIs. Aim: To detect pathogens associated with STIs in symptomatic men and its relationship with sexual behavior. Methodology: DNA was obtained from exfoliated cells of penis from 20 symptomatic men. Pathogens were detected using qPCR or PCR followed by reverse line blot. Sexual behavior was evaluated through a survey. Results: Two or more infectious agents were detected in 50% of samples. U. urealyticum was found in 25%, meanwhile C. trachomatis and M hominis were detected in 15%. VHS-1, VHS-2 and M genitalium were detected only in 5%. HPV was found in all samples. The most frequent HPV genotypes were VPH 16, 11, 70. There were no statistical link found between sexual behavior and the studied microorganisms Conclusion: Infectious agents associated with STIs were detected in symptomatic men. HPV was the most frequent pathogen and it was detected in multiple genotypes. It is necessary to increase the sample size to associate significantly the sexual behavior with the results.