The effects of El Niño-induced droughts on dipterocarp forests must be quantified to evaluate the implications of future global climatic changes for the tropical forests of Southeast Asia. We studied the mortality of trees ≥ 1 cm in diameter in a lowland dipterocarp forest in Borneo before, during, and after the 1997/1998 El Niño drought. The annual mortality rates were 1.30, 1.75, and 1.66 percent/yr for the pre-drought, drought, and post-drought periods, respectively. The effect of drought was tree size-dependent being greater for larger trees. Modified logistic regression analysis revealed a significant interaction effect between species' habitat association and edaphic condition on mortality rates in all periods. For species associated with wet habitat, drought effect was greater in dry conditions than in wet conditions, in both the drought and post-drought periods. The mortality rates of dry-habitat species were less affected by the drought both in dry and wet conditions. A similar pattern was also found in common Dipterocarpaceae species; mortality rates increased more in species associated with wet-habitat in the drought and post-drought periods. Species and families with higher mortality in the pre-drought period tended to experience greater mortality increases during the drought and post-drought periods. These results suggest that changes in drought regimes alter the species composition and spatial distribution of dipterocarp forests.