Patterns of vertical stratification and canopy utilization by rodents and marsupials were analysed in two contiguous Atlantic forests at different altitudes (100 m and 900 m asl). Twenty-two species were captured using live traps placed at ground level, in the understorey (1.5–2.0 m), and in the canopy (6–15 m) over 2 y; seven species (32%) were mainly or exclusively arboreal. Community composition and relative abundance of species in the different vertical strata were not similar, with a general reduction in the number of species, and in abundance in the upper layers. The following species were captured mainly or exclusively in the canopy: Micoureus demerarae and Gracilinanus microtarsus (Didelphimorphia, Didelphidae); Wilfredomys pictipes, Oecomys aff. concolor, and Rhipidomys aff. macrurus (Rodentia, Muridae); and Nelomys nigrispinus (Rodentia, Echimyidae). Our results indicated that altitudinal changes in Atlantic forest areas may alter the community composition of different forest layers but they do not seem to alter greatly specific patterns of vertical habitat utilization. Similar-sized species tended to differ in their patterns of vertical utilization of habitat with the exception of terrestrial akodontine rodents (genera Akodon, Thaptomys, Oxymycterus and Brucepattersonius). Rodents (mainly Oryzomys russatus) dominated captures at ground level at both sites but Akodontinii were numerous only at the highest site. Unlike other neotropical forests, marsupials did not dominate canopy captures.