Most neurons of the central complex belong to 10 secondary (larvally produced) lineages. In the late larva, undifferentiated axon tracts of these lineages form a primordium in which all of the compartments of the central complex can be recognized as discrete entities. Four posterior lineages (DPMm1, DPMpm1, DPMpm2, and CM4) generate the classes of small-field neurons that interconnect the protocerebral bridge, fan-shaped body, noduli, and ellipsoid body. Three lineages located in the anterior brain, DALv2, BAmv1, and DALcl2, form the large-field neurons of the ellipsoid body and fan-shaped body, respectively. These lineages provide an input channel from the optic tubercle and connect the central complex with adjacent anterior brain compartments. Three lineages in the posterior cortex, CM3, CP2, and DPMpl2, connect the posterior brain neuropil with specific layers of the fan-shaped body. Even though all of the compartments of the central complex are prefigured in the late larval brain by the axon tracts of the above-mentioned lineages, the neuropil differentiates during the first 2 days of the pupal period when terminal branches and synapses of secondary neurons are formed. During this phase the initially straight horizontal layers of the central complex bend in the frontal plane, which produces the characteristic shape of the fan-shaped and ellipsoid body. Our analysis provides a comprehensive picture of the lineages that form the central complex, and will facilitate future studies that address the structure or function of the central complex at the single cell level. J. Comp. Neurol. 519:661–689, 2011. © 2010 Wiley-Liss, Inc.