Men who have sex with men (MSM) attending sexual health (SH) clinics are at high risk for HIV acquisition and are disproportionately affected by sexually transmitted infections (STIs). We collected standardised behavioural data from MSM attending clinics to characterise sexual behaviours and identify predictors for HIV and STIs. In 2012–2013, HIV-negative MSM attending five SH clinics in England reported sexual behaviours in the previous three months via a self-administered questionnaire. Behaviours were linked to the individual’s clinical records using national surveillance. The prevalence and incidence of bacterial STIs (gonorrhoea, Chlamydia, lymphogranuloma venereum and syphilis) and incidence of HIV were calculated. Adjusted odds ratios and hazard ratios with 95% confidence interval (CI) were reported for significant predictors. Of 1278 HIV-negative MSM, 54% were of white ethnicity and UK-born and 43% were 25–34 years old. Almost all men reported at least one partner in the last three months. Half reported condomless anal sex and 36% condomless receptive anal intercourse (CRAI). Incidence of bacterial STIs was 46/100 (95%CI 39–54) person years (py) and of HIV was 3.1/100 (95%CI 1.7–5.6) py. A STI at baseline and CRAI with increasing numbers of partners were associated with both incident infections. In this cohort of MSM high-risk behaviours and STIs were prevalent. Engagement in CRAI increased the likelihood of subsequent infection, while men diagnosed with a bacterial STI were at increased risk of a future STI. Clinical and behavioural risk assessments to determine an individual’s risk of infection could allow a more nuanced prevention approach that has greater success in reducing transmission.