Phylogenetically conserved brain centers known as mushroom bodies are implicated in insect associative learning and in several other aspects of insect behavior. Kenyon cells, the intrinsic neurons of mushroom bodies, have been generally considered to be disposed as homogenous arrays. Such a simple picture imposes constraints on interpreting the diverse behavioral and computational properties that mushroom bodies are supposed to perform. Using a P[GAL4] enhancer-trap approach, we have revealed axonal processes corresponding to intrinsic cells of the Drosophila mushroom bodies. Rather than being homogenous, we find the Drosophila mushroom bodies to be compound neuropils in which parallel subcomponents exhibit discrete patterns of gene expression. Different patterns correspond to hitherto unobserved differences in Kenyon cell trajectory and placement. On the basis of this unexpected complexity, we propose a model for mushroom body function in which parallel channels of information flow, perhaps with different computational properties, subserve different behavioral roles.