We present a study of the endemicity patterns in the Brazilian Atlantic Forest on the basis of the distribution of 107 fly species belonging to 24 genera of 15 families. This is the first picture of endemism for Diptera in the Atlantic Forest. Instead of the traditional grid of geographical coordinates, we used a system of topographic units (TUs) for the analysis, delimited after gathering information on rivers and altitude for each state and country. A parsimony analysis of the data matrix with the species records for the TUs was performed, named topographic-unit parsimony analysis (TUPA). The same distributional data was used in a NDM/VNDM analysis. The combination of the resulting patterns from both analyses indicated the existence of the following three major areas of endemism for flies in the Atlantic Forest: a Northern Atlantic Forest, north of Rio Doce; a Southern Atlantic Forest, south of Rio Doce along the coast, extending to the west and to the south at the level of the state of Paraná; and a Semideciduous Seasonal Forest, west to the ombrophilous forest along the coast. None of these areas seems to be shaped solely by vicariance events. They can possibly be the result of biotic fusion of ancestral areas of endemism as a result of barrier collapse and secondary overlap of sister biotas, a hypothesis yet to be tested. The recognition of a separate area of endemism for flies in the Semideciduous Forest agrees with phytogeographical reconstructions and raises an important alert for the scarcity of biological reserves for this vegetation.