Men who have sex with men (MSM) are at higher risk for co-infection with hepatitis B virus (HBV), hepatitis C virus (HCV) than the general population. The co-infection accelerates disease progressionreciprocally. This study purposed to investigate the prevalence and the associated factors with HBV and/or HCV co-infection with HIV among MSM in Northern region Thailand in 2015. A case-control study design was conducted by a hospital-based in anti-retroviral (ARV) clinic. 31 of 51 hospitals in the Phayao, Chiang Mai and Chiang Rai province were recruited in this study. The result was found 374 total participants who were registered patients in ARV clinic inPhayao84 cases (22.5 %), Chiang Mai 170 (45.5%) and Chiang Rai120 (32.1%). The participants were 30-43 year old (47.1%), followed by 16-29 years old (29.9%), and 44-57 years old (19.8%). The majority of occupational were employee (50.0%), follow by merchant (24.9%) and agriculturist (9.4%).The univariate analysis with a significant α level of 0.05were found six factors had significantly association with HBV and/or HCV with HIV co-infection including (1) age range (2) smoking behavior (3) tongue piercing, (4) Stavudine drug taking, (5) Tenofivir drug taking and (6) Nevirapine drug taking. Moreover, the binary logistic regression at a significant α level of 0.05, after controlling for all possible confounding factors, were found four factors significantly association with co-infection including (1) age between 30-43 year old had the risk of co-infection 2.42 times [odds ratio (OR) = 2.42, 95% confidence interval (CI) = 1.14-5.14] higher than those who had age range 16-29 year old, (2) smoking behavior in the participants had the risk of co-infection 2.05 times (OR = 2.05, 95% CI = 1.12-3.76) higher than no smoking behavior. (3)Tongue piercing in the participants had the risk of co-infection 6.82 times (OR = 6.70, 95% CI = 1.12-40.19) higher than no tongue piercing and (4) Tenofivir drug taking had the risk of co-infection 4.30 (OR = 4.30, 95% CI = 2.37-7.84) more than no taking drug. Therefore, enhancing the surveillance and targeted prevention of viral hepatitis including improved disease prevention, vaccination coverage, sanitation and food safety, safer sex and efficiency healthcare delivery,