The Indonesian province of East Kalimantan is home to some of the largest remaining contiguous tracts of lowland Dipterocarp forest on the island of Borneo. Nest surveys recently conducted in these forests indicated the presence of a substantial population of Eastern Bornean orangutans (Pongo pygmaeus morio) in the Berau and East Kutai regencies in the northern half of the province. The Sangkulirang Peninsula contains extensive limestone karst forests in close proximity to the lowland Dipterocarp forests inhabited by orangutans in these regencies. Orangutans have been sighted in these limestone karst forests, but the importance of this forest type for orangutans has been unclear. Therefore, we conducted 49 km of nest surveys in limestone karst forest to obtain the first quantitative estimates of orangutan densities in this habitat, and walked 28 km of surveys in nearby lowland Dipterocarp forests for comparison. We also gathered basic ecological data along our transects in an attempt to identify correlates of orangutan abundance across these habitat types. Undisturbed limestone karst forests showed the lowest orangutan densities (147 nests/km(2), 0.82 indiv/km(2)), disturbed limestone forests had intermediate densities (301 nests/km(2), 1.40 indiv/km(2)), and undisturbed lowland Dipterocarp forests contained the highest density (987 nests/km(2), 5.25 indiv/km(2)), significantly more than the undisturbed limestone karst forests. This difference was not correlated with variation in liana abundance, fig stem density, or stump density (an index of forest disturbance). Therefore, other factors, such as the relatively low tree species diversity of limestone karst forests, may explain why orangutans appear to avoid these areas. We conclude that limestone karst forests are of low relevance for safeguarding the future of orangutans in East Kalimantan.