Some men who have sex with men (MSM) were assigned female at birth (AFB) and/or identify as trans men. Little is known about how these men differ from other MSM. We compared sexual and mental health indicators from the European MSM Internet Survey (EMIS-2017), comparing men AFB and/or currently identifying as trans men with those assigned male at birth (AMB) who identified as men. EMIS-2017 was an opportunistic 33-language online sexual health survey for MSM recruiting throughout Europe. We used regression models adjusting for age, country of residence and employment status to examine differences across groups. An analytic sample of 125,720 men living in 45 countries was used, of which 674 (0.5%) were AFB and 871 (0.7%) identified as trans men. The two sub-groups were not coterminous, forming three minority groups: AFB men, AFB trans men and AMB trans men. Minority groups were younger and more likely unemployed. Anxiety, depression, alcohol dependence and sexual unhappiness were more prevalent in sex/gender minority men. Conversely HIV and STI diagnoses were less common. AMB trans men were most likely to have sexual risk behavior with steady partners and to have unmet health promotion needs, and were least likely to be reached by interventions. Sex assigned at birth and trans identification were associated with different sexual and mental health needs. To facilitate service planning and to foster inclusion, sex-assigned-at-birth and current gender identity should be routinely collected in health surveys.