Female genital cutting (FGC) is a widespread cultural practice in Africa, with a number of potential adverse health consequences for women. International organisations, national governments together with NGOs, community-based and grass-root organisations are trying to reduce the prevalence of FGC. Despite these efforts, female genital cutting is still a widespread phenomenon. It was hypothesised by Kun (1997) that FGC increases the risk of HIV transmission through a number of different mechanisms. Yount and Abraham (2007) in their detailed analysis of 2003 Kenyan Demographic and Health Survey reported that FGC is not directly associated with HIV but indirectly through several pathways. We applied multilevel analysis on the same dataset to demonstrate that there is a significant direct and positive association between FGC and HIV after controlling for hierarchical structure of the data, potential confounding factors, and interaction effects. FGC increases the odds of being HIV positive by the factor of 4.17 when compared to women without FGC. Furthermore, the results show that women who had FGC and older first union partners have higher odds of being HIV positive than their counterparts (odds further changes by the factor of 1.66); the odds of being HIV positive increase further by the factor of 2.27 if women reported having a genital ulcer. These results suggest the underlying complex interplay of biobehavioural and social variables in disentangling the association between FGC and HIV.