Trans persons, including transvestites and transsexual women, show disproportionately high HIV/AIDS rates when compared to the rest of the population. However, few quantitative/qualitative studies have addressed trans persons in Brazil. Thus, a team of researchers from different fields is developing an interdisciplinary research project with the objective of shedding light on living conditions and ways of life among transvestites and transsexual women, while investigating determinant factors for HIV infection, syphilis, and hepatitis B and C. The article is intended to describe the experience with the implementation and development of an ethno-epidemiological study in Salvador, Bahia State, Brazil. Mapping the population began with a formative survey that was crucial for orienting the epidemiological survey. The production of ethno-epidemiological data posed a daily challenge for the researchers, triggering a series of reflections on the limits of our concepts and categories for translating the diversity of study participants’ practices and experiences.