AbstractIn this study, we have analyzed the architecture of the brain neuropile of the Drosophila larva, which is formed by two main structural elements: long axon tracts and terminal axonal/dendritic arborizations carrying synapses. By using several molecular markers expressed in neurons and glial cells, we show that the early larval neuropile is subdivided by glial sheaths into numerous compartments. The three‐dimensional layout of these compartments and their relationship to the pattern of long axon tracts described in the accompanying article (Nassif et al. [2003] J. Comp. Neurol 417–434) was modeled by using a three‐dimensional illustration computer software. On the basis of their location relative to each other and to long axon tracts, larval brain compartments can be identified with compartments defined by structural and functional criteria for the adult fly brain. We find that small precursors of most of the compartments of the adult central brain can be identified in the early larva. Changes in brain compartmental organization occurring during larval growth are described. Neuropile compartments, representing easily identifiable landmark structures, will assist in future analyses of Drosophila brain development in which the exact location of neurons and their axonal trajectories is of importance. J. Comp. Neurol. 455:435–450, 2003. © 2002 Wiley‐Liss, Inc.