Data from the Botswana Aids Impact Survey II (BAIS II) is used to find the components difference in HIV prevalence rates between four selected districts; Chobe, Kweneng-West, CentralSerowe and Ghanzi. The techniques of standardisation and decomposition are used to compare the differences in HIV prevalence rates across the districts, and to find the difference in HIV prevalence rates because of the effects of the rate and compositional factors. The analysis takes four confounding variables into account, namely age, sex, education and marital status. Our findings show that the factor specific rate and the compositional factor effects contributed differently to the difference in the observed HIV rates between any two districts. In particular, the large effect in the observed HIV rates between any two districts comes from the contribution of the adjusted rate and the age component. Secondly, the HIV prevalence rate remained higher in Chobe district compared to the other three districts. It is not clear why HIV prevalence rate is patterned by age and less by the other three factors. Our overall conclusion is that age composition is important when comparing differences in district HIV prevalence rates. The other three factors are not able to explain regional difference in HIV prevalence because of their disproportionate distribution across the districts under study. Future studies could analyse these three factors separately, and explore other individual and lifestyle factors. The extent to which these factors explain differences in the prevalence rate of HIV between two populations over time, as well as how real change occurs, may also be established.