To analyze sorting and compartmentalization of molecules in neuronal endomembranes, the distribution of endogenous proteins associated with the endoplasmic reticulum (ER), intermediate compartment, the Golgi apparatus in cultures of dorsal root ganglion (DRG), and hippocampal neurons was compared with that of newly synthesized ER-associated rotavirus proteins. The endogenous ER-retained immunoglobulin heavy chain binding protein, protein disulfide isomerase, and a peptide containing the KDEL amino acid sequence appeared in the soma and dendrites up to their first branching, but not in axons. However, two other endogenous ER-associated proteins, calreticulin and calnexin, occurred in axons as well as in the somatodendritic domains. The ER-associated rotavirus proteins, VP7 and NSP4, were widely distributed in cell bodies and dendrites. The former appeared also in axons and its localization partially overlapped with that of calreticulin and calnexin. One intermediate compartment protein, ER-Golgi-intermediate compartment-protein-53 (ERGIC-53), extended beyond the first division of the dendrites and did not, as the small guanosine 5'-triphosphate (GTP)-binding protein rab2, appear in axons. The location of rab2 to small vesicles was distinct from that of rotavirus VP7. Cis/medial Golgi cistern proteins were restricted to the cell bodies and proximal dendrites. This study emphasizes the marked heterogeneity in the targeting to axons and dendrites of proteins associated with ER and intermediate compartments. Therefore, the composition of axonal ER-retained molecules differs from that in the soma and this variation may reflect differences in functions between the ER compartments. Viral proteins are useful reporters for such heterogeneities and rotavirus VP7 may be a tool to reveal sorting signals for targeting of vesicular proteins to axons via a nonclassical Golgi-independent mechanism. Such signals may also determine viral targeting to different regions of the brain.