This article draws on the work of Michel Foucault to critique epidemiological methods in general and transgender HIV prevention research in particular. Funding for transgender HIV prevention research and programs is often directly connected to widely accepted, yet often problematic, practices of data collection and analysis. The authors believe that attending to the needs of those who do not conform to a binary gender system requires analyzing the ways in which epidemiology research produces and reifies the gender system itself. In order to understand the relation between a trans “identity” and a trans “population,” the article employs as analytics Foucault's concepts of normalizing power and biopower. It reviews the history and techniques of epidemiology and then briefly the ways in which normalizing power produces specific identity categories such as gender and gender identity as inherent to an individual, followed by an examination of how those socially produced identities operate at the level of population regulation. Finally, it explores some resistant practices that both epidemiologists themselves and the targets of their research might engage in order to at least mitigate some of these difficulties.