The HIV/AIDS pandemic is considered a security threat. Policy-makers have warned of destabilization of militaries due to massive troop deaths. Estimates of the rate of HIV within African militaries have been as high as 90 per cent. We aimed to determine if HIV prevalence within African militaries is higher than their host nation prevalence rates. Using systematic searching and access to United States Department of Defense data, we abstracted data on prevalence within militaries and their host communities. We conducted a random effects pooled analysis to determine differences in HIV prevalence rates in the military versus the host population. We obtained data on 21 African militaries. In general, HIV prevalence within the military is elevated compared to the general population. The differences were significant (odds ratio 1.97, 95% confidence interval: 1.58-2.45, P < 0.001). Further, inflated rates of HIV in militaries compared to non-military males of similar age were also significant (6.09, 4.47-8.30, P < or = 0.0001). States with recent conflicts and wars had elevated military rates, but these were also not significant (P = 0.4). Population levels predicted military prevalence rates (P < or = 0.001). HIV/AIDS prevalence rates in most African militaries are significantly elevated compared to their host communities.