Despite methodological and theoretical advances in conservation genetics, data on genetic variation on broad regional spatial scales are still scarce, leading conservation planners to use general heuristic or simulation models for an integrated analysis of genetic, demographic and landscape parameters. Here, we extended previous results by evaluating spatial patterns of extinction by inbreeding depression under stochastic variation of environments for mammalian populations in 31 conservation units of the Brazilian Cerrado. We observed a large spatial variation of times to extinction, for different conservation units and body-size classes of species. For small-bodied species (500 g), the population times to extinction in the conservation units were usually longer than 200 years, whereas for medium-bodied (5 kg) and large-bodied (50 kg) species this time was considerably shorter, and only a few units would maintain viable populations for more than 100 years. These figures are consistent with the current status of mammalian conservation in Brazil, and hopefully the simulated scenarios can be integrated to patterns of human occupation and habitat loss in the biome, in order to furnish overall guidelines for biodiversity conservation.