This paper evaluates the ecological consequences of hunting by comparing mammalian densities, biomass, relative energy consumption and community structure between sites with different levels of hunting pressure. Hunting is carried out mainly by colonists who farm on the edge of Atlantic forest fragments in the State of São Paulo, Brazil. Mammals were studied over a period of 18 months, along 2287 km of line transects. Transects were distributed among two protected sites, one slightly hunted site and two heavily hunted sites. Tapirs, the two peccary species, brocket deer, armadillos and agoutis are preferred by hunters in the region. Primates are not hunted in the region. Hunting has affected community structure, with ungulates dominating mammalian biomass at protected sites and primates dominating at hunted sites. This has caused an ecological inversion in the hunted areas of the Atlantic forests. In Amazonian regions of the Neotropics hunting is more evenly distributed among primates, large rodents, and ungulates and has resulted in an opposite inversion, with hunted sites having lower primate biomass. Atlantic forests are very susceptible to the possible ecological imbalances induced by hunting by humans, and this must be considered for management and conservation programmes.