Abstract Background The continued depletion of tropical rainforests and fragmentation of natural habitats has led to significant ecological changes which place most top carnivores under heavy pressure. Various methods have been used to determine the status of top carnivore populations in rainforest habitats, most of which are costly in terms of equipment and time. In this study we utilized, for the first time, a rigorous track classification method to estimate population size and density of clouded leopards ( Neofelis nebulosa ) in Tabin Wildlife Reserve in north-eastern Borneo (Sabah). Additionally, we extrapolated our local-scale results to the regional landscape level to estimate clouded leopard population size and density in all of Sabah's reserves, taking into account the reserves' conservation status (totally protected or commercial forest reserves), their size and presence or absence of clouded leopards. Results The population size in the 56 km 2 research area was estimated to be five individuals, based on a capture-recapture analysis of four confirmed animals differentiated by their tracks. Extrapolation of these results led to density estimates of nine per 100 km 2 in Tabin Wildlife Reserve. The true density most likely lies between our approximately 95 % confidence interval of eight to 17 individuals per 100 km 2 . Conclusion We demonstrate that previous density estimates of 25 animals/100 km 2 most likely overestimated the true density. Applying the 95% confidence interval we calculated in total a very rough number of 1500–3200 clouded leopards to be present in Sabah. However, only 275–585 of these animals inhabit the four totally protected reserves that are large enough to hold a long-term viable population of > 50 individuals.