Introduction: Gonorrhea (GC) infection caused by Neisseria gonorrhoeae has been steadily increasing in Thailand over the last decade. Men who have sex with men (MSM) are at high risk for gonorrhea infection. Materials and methods: In this study, we determined the prevalence of and risk factors associated with gonococcal infections by three anatomical sites among MSM. We have conducted a cross-sectional analysis of a sexually transmitted disease (STD), gonorrhea among MSM attending two STD clinics in Khon Kaen, Thailand. We included 358 MSM over 18 years of age. Data were collected using self-administered questionnaire. In each participant, an oropharyngeal, anorectal, and endourethral swab were tested with culture and nucleic acid amplification test (NAAT). However, 267 urine samples were tested by both methods. Factors associated with gonorrhea infections were assessed using univariate and multivariate logistic regression. Results: One hundred and ninety-five out of 358 (54.47%) MSM tested were found to be positive for gonorrhea using a porA gene targeted NAAT by Real-time PCR with TaqMan probes, but there was no positive result by culture. The gonorrheal prevalence for male genital site, anal, and oropharyngeal, were 34.73% (95%CI 33.07, 45.08), 29.01% (95%CI 24.61, 34.33), and 27.93% (95%CI 23.35, 32.89), respectively, while 5.9% (21/355) were positive for gonococcal infection in all anatomic sites (oropharynx + anus + urethra) of one participant. Previous history of diagnosed STDs was a significant factor associated urethral gonorrhea (odds ratio = 3.52, 95%CI 1.87-6.66, P Value< 0.001). In addition, having more than one partner was increased urethral gonorrhea (adjusted odds ratio = 2.26, 95%CI 1.10-4.68, P Value=0.026). 100% of condom use was found decreasing urethral infection (adjusted odds ratio = 0.39, 95%CI 0.15-0.99, P Value=0.046). Conclusions: The most common anatomic site of gonorrhea infection was male genital site, and the independent risk factors were having history of diagnosed STDs and having more than one partner in the past 3 months, but 100% condom use was a protective factor of this infection.