Information about the input and output pathways of higher-order brain neuropils is essential for gaining an understanding of their functions. The present study examines the connectivity of two higher-order neuropils in the central olfactory pathway of the crayfish: the accessory lobe and its target neuropil, the hemiellipsoid body. It is known that the two subregions of the accessory lobe, the cortex and medulla, receive different inputs; the medulla receives visual and tactile inputs, whereas the cortex receives neither (Sandeman et al.  J Comp Neurol 352:263–279). By using dye injections into the olfactory lobe, we demonstrate that the accessory lobe cortex and medulla also have differing connections with the olfactory lobe. These injections show that local interneurons joining the olfactory and accessory lobes branch primarily within the cortex with only limited branching within the medulla. Injections of different dyes into the two subregions of the hemiellipsoid body, HBI and HBII, show that the accessory lobe cortex and medulla also have separate output pathways. HBI is innervated by the output pathway from the cortex while HBII is innervated by the output pathway from the medulla. These injections also show that HBI and HBII are innervated by separate populations of local interneurons with differing connections to higher-order neuropils in the olfactory and visual pathways. These results suggest a segregation of olfactory and multimodal (including olfactory) inputs within both the accessory lobe and the hemiellipsoid body and provide evidence of important functional subdivisions within both neuropils. J. Comp. Neurol. 481:118–126, 2005. © 2004 Wiley-Liss, Inc.