Background Risky health behaviours play a role in the individual being able to spread the HIV/AIDS disease to others. HIV risk behaviours are therefore a major reproductive and public health concern, especially with the HIV epidemic.Methods The purpose of this study was to estimate the prevalence of the HIV risk behaviours and factors associated with risk behaviours among married and cohabitating individuals in Botswana. The study was based on data from the 2013 Botswana AIDS Impact Survey. The study population comprised 2503 cases of married and cohabitating individuals aged 20-64 years. Descriptive and logistic regression analyses were used to examine the predictors of HIV risk behaviours.Results The HIV risk behaviour index results show that high-risk behaviour was highest among married individuals (56.2%) compared to those cohabiting (39.2%). Statistically, significant association was observed in the pooled sample in which the married were more than two times (AOR = 2.251, 95% CI: 1.794-2.823) more likely to engage in risky behaviour than their cohabiting counterparts. Moreover, the odds of engaging in HIV risk behaviour were significantly high among cohabiting people who reported alcohol use (AOR = 1.500; 95% CI: 1.250-2.485) and had tested for HIV (AOR = 2.282; 95% CI: 1.282-3.509). Quite conversely, among the married respondents with tertiary education the odds of engaging in risky sexual behaviour were significantly low (AOR = 0.663, 95% CI: 0.472-0.930). All comparisons were statistically significant at p < 0.05.Conclusions In conclusion, the results show that HIV risk behaviours are prevalent among the married and cohabiting population in Botswana. Therefore, policies and programmes relating to issues such as gender inequality and alcohol consumption should be target-specific to address the married and cohabiting individuals.