Background Sexually transmitted infections are the major problems among most high risk population of HIV and AIDS in Nepal. Studies were showed Men having sex with men and transgender has higher risk of HIV and STI in the eastern of Nepal.

Methods The cross-sectional descriptive studies conducted among 156 MSM and transgender in the eastern region of Nepal. The clinical examination and syndromic informations were taken through checklist and questionnaire was asked to assess the risk behaviour. The verbal consent was taken from the respondents.

Results Fifty six percent of respondents didn’t use condom and lubricants during their sexual intercourses. One quarter of respondents didn’t hear about lubricants. Fifteen percent of them did sexual contact after taking alcohol and most of them didn’t care about their correct process of condom application. Twenty percent of respondents have more than two sexual partners which they had to involve in sexual intercourse at least two times in the months. The use and non use of condom is associated with the STI incidence (P = 0.001, α = 5). Among the total respondents forty percent had at least one symptoms of STI such as urethral and anal discharge, genital wart, itching and ulceration. Most of the respondents feared to go to the doctors because of social stigma.

Conclusion STI among MSM and Transgender was higher. The social acceptance was low. The MSM and Transgenders should encourage attending STI clinics for their sexual problems remedies.