Objectives Continuing high STI positivity among men who have sex with men (MSM) attending centres for sexual health (CSH) indicates that high-risk behaviour is ongoing. The objective of this study was to gain a better insight into risk behaviours among MSM attending CSH and to explore STI and HIV positivity by subgroups. Methods We used national data routinely collected during CSH consultations for this study. From September to December 2017, questions on group sex, substance use and sex with HIV-positive partners were asked at each CSH consultation. We analysed latent classes of client-related factors and sexual risk behaviour among MSM attending CSH in this period. We examined STI positivity and prevalence ratios by latent classes. Results A total of six classes were identified in order of increasing risk: ‘overall low-risk behaviour’ (n=2974; 22.0%), ‘Western origin and multiple sex partners’ (MSP) (n=4182; 30.9%), ‘Non-Western origin and MSP’ (n=2496; 18.5%), ‘living with HIV’ (n=827; 6.1%), ‘group sex and HIV-positive partners’ (n=1798; 13.3%) and ‘group sex and chemsex’ (n=1239; 9.2%). The any STI positivity ranged from 14.0% in the overall low-risk behaviour class to 35.5% in the group sex and chemsex class. HIV positivity did not differ significantly between classes. The Western origin and MSP class was largest and accounted for the majority of STI and HIV infections. Conclusions Although STI positivity increased with increased risky behaviours, considerable STI positivity was found in all six latent classes. Comparable HIV positivity between classes indicates risk reduction strategies among subgroups engaged in risky behaviours. The differences in risk behaviour and STI positivity require preventive strategies tailored to each subgroup.