This revealed seven epidemiologic puzzles involving officially reported trends and conspicuously missing information. I used primarily ethnographic methods while drawing upon epidemiology, and compared government surveillance data to observations at community and institutional sites (459 pages of field notes 175 persons observed), qualitative interviews with stakeholders in local HIV epidemics ( n = 32), and document research ( n = 116). I used a ground truthing conceptual framework to meet two aims: first, to determine how accurately official surveillance data represented Japan's two largest epidemics (urban Kansai and Tokyo) as understood and experienced on the ground and second, to identify explanations for why the HIV epidemics were unfolding as officially reported. Japan is widely perceived to have a low level of HIV occurrence however, its HIV epidemics also have been the subject of considerable misunderstanding globally.