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Abstract Background To date, research on men who have sex with men (MSM) has largely focused on their sexual health needs and on men recruited from gay-orientated venues. National probability survey data provide a rare opportunity to examine the broader sociodemographic, behavioural, and health profiles of MSM, defined as men who reported ≥1 male sexual partner(s) in the past 5 years, and thus regardless of their sexual identity, in comparison to men reporting sex exclusively with women (MSEW) during this time, and also the extent that health inequalities cluster. Methods Britain’s third National Survey of Sexual Attitudes and Lifestyles (Natsal-3), a probability sample survey, interviewed 15,162 people aged 16–74 years (6,293 men) during 2010–2012 using computer-assisted personal-interviewing with a computer-assisted self-interview. We used multivariable regression to compare MSM relative to MSEW in their reporting of variables, individually and collectively, corresponding to three domains: physical, mental, and sexual health. Results Among all men, 2.6 % (n = 190) were defined as MSM, of whom 52.5 % (95 % CI: 43.6 %–61.2 %) identified as gay. MSM were as likely as MSEW (n = 5,069) to perceive their health was ‘bad’/’very bad’, despite MSM being more likely to report a long-standing illness/disability/infirmity (adjusted odds ratio, AOR: 1.46, 95 % CI:1.02–2.09), treatment for depression/past year (2.75, 1.69–4.47), and substance use (e.g., recreational drug use/past year: 3.46, 2.22–5.40). MSM were more likely to report harmful sexual health behaviours, e.g., condomless sex with ≥2 partners/past year (3.52, 2.13–5.83), and poor sexual health outcomes, including STI diagnosis/es (5.67, 2.67–12.04), poorer sexual function (2.28, 1.57–3.33), both past year, and ever-experience of attempted non-volitional sex (6.51, 4.22–10.06). MSM were also more likely than MSEW to report poor health behaviours and outcomes both within and across the three health domains considered. Of all MSM, 8.4 % had experienced poor health outcomes in all three domains – physical, mental, and sexual health - in contrast to 1.5 % of all MSEW. Conclusions MSM are disproportionately affected by a broad range of harmful health behaviours and poor health outcomes. Although often observed for a minority of MSM, many health inequalities were seen in combination such that policies and practices aimed at improving the health and well-being of MSM require a holistic approach, regardless of clinical specialty.