Knowledge of distributional patterns and areas of endemism (AE) is an important source to protect the biodiversity. The Atlantic Forest (AF) is the second major rainforest of the Americas, and combining an extensive latitudinal range with altitudinal gradient, hosts one of the most important faunal diversities of the world, here highlighted by the high diversity of non-volant small mammals. However, the AF is one of the more threatened biomes, with significant habitat loss to urbanisation and expansion of agricultural frontiers. Based on 283 inventory records of 105 species of small mammals we employed parsimony analysis of endemicity (PAE) and endemicity analysis (EA) implemented in the programs NDM and VNDM to delimitate AEs in the AF. Using 25% for radius to fill and 50% to radius to assume, the PAE results show 11 individual AEs and nine consensus AE. For EA analyses, using the grid size of 0.75° with two points, we detect 15 areas of endemism. Ours results indicate that nine of them are congruent AE. Our results highlighted the following AE: Misiones; coastal Southern; Serra do Mar; Highlands of Espirito Santo and Minas Gerais; coastal Northeastern. Most of these areas are within conservation units and have already been identified as AE for other vertebrates, highlighting their importance for the maintenance of biodiversity. However, we also have identified unprotected areas that deserve priority attention. The AEs identified here represent a major advance in mammal quantitative distribution patterns in the AF, contributing to biogeography studies and conservation planning.