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Men who have sex with men (MSM) are at greater risk for sexually transmitted infections (STIs). Data on MSM chlamydia and gonorrhea prevalence estimates and associated risk factors are scarce. To our knowledge, this is the first study to describe the prevalence and the determinants of both chlamydia and gonorrhea infections in MSM in Portugal. We conducted a cross-sectional study using data from 1832 visits to CheckpointLX, a community-based center for screening blood-borne viruses and other STIs in MSM. Overall prevalence of chlamydia or gonorrhea in our sample was 16.05%, with 14.23% coinfection and 40.73% asymptomatic presentation among those testing positive. Anorectal infection was most common for chlamydia (67.26%), followed by urethral (24.78%) and oral (19.47%) infection. Oral infection was most common for gonorrhea (55.63%), followed by anal (51.25%) and urethral (17.50%) infection. In multivariate analyses, young age (U = 94684, p = 0.014), being foreign-born (χ2 = 11.724, p = 0.003), reporting STI symptoms (χ2 = 5.316, p = 0.021), inhaled drug use (χ2 = 4.278, p = 0.039) and having a higher number of concurrent (χ2 = 18.769, p < 0.001) or total (χ2 = 5.988, p = 0.050) sexual partners were each associated with higher rates of chlamydia or gonorrhea infection. Young and migrant MSM are a vulnerable population to STIs, as are those who use inhaled drugs and those with a higher number of concurrent or total sexual partners. Although Portugal has no guidelines on chlamydia and gonorrhea screening, our results point toward a need for greater awareness about the importance of high-frequency screening for those at increased risk (i.e., every three to six months). [ABSTRACT FROM AUTHOR]