Though sometimes controversial, there is growing consensus that human general intelligence is associated with variation in a number of aspects of cortical organization including brain volume, white and gray matter volume, connectivity, and cortical thickness. Recent studies in great apes have shown, like humans, they exhibit both general and domain specific forms of intelligence when tested on a wide range of cognitive tests; however, whether individual variation in intelligence is associated with measures of cortical organization remains untested. Here we show that general intelligence in chimpanzees is associated with total brain volume, total gray matter volume, mean cortical thickness and regional variation in both gray matter volume and cortical thickness. These results suggest that increased gray matter volume and cortical thickness may produce enhanced computational cognitive processes and may have been selected for during primate brain evolution.