We examine the performance of the primary school education system in Tanzania over the 1990s - a decade characterized by substantial AIDS deaths. Given the relatively robust correlation between educational attainment and productivity established in the literature in both agricultural and non-agricultural sectors, human capital accumulation through education forms a major component of development strategy. At the same time, AIDS poses clear threats to the goal of human capital accumulation through education. To assess performance of the primary school system, we estimate non-stationary education transition matrices using a minimum cross entropy approach at the national, sub-national, and regional levels for girls, boys, and all students. Results indicate a deterioration in primary school performance using enrollments in grade 7, the final year of primary school, as a metric. This deterioration in performance occurred despite increased real resource allocations to the public education system and positive, if only tepid, overall economic growth trends. We conclude that the HIV/AIDS pandemic has quite likely slowed human capital accumulation in Tanzania.