Extensive research has revealed a fundamental organization of the cerebellum consisting of functional parasagittal zones. This compartmentalization has been well documented with respect to physiology, biochemical markers, and climbing fiber afferents. Less is known about the organization of mossy fiber afferents in general, and more specifically in relation to molecular markers such as zebrin. Zebrin is expressed by Purkinje cells that are distributed as a parasagittal array of immunopositive and immunonegative stripes. We examined the concordance of zebrin expression with visual mossy fiber afferents in the vestibulocerebellum (folium IXcd) of pigeons. Visual afferents project directly to folium IXcd as mossy fibers and indirectly as climbing fibers via the inferior olive. These projections arise from two retinal recipient nuclei: the lentiformis mesencephali (LM) and the nucleus of the basal optic root (nBOR). Although it has been shown that these two nuclei project to folium IXcd, the detailed organization of these projections has not been reported. We injected anterograde tracers into LM and nBOR to investigate the organization of mossy fiber terminals and subsequently related this organization to the zebrin antigenic map. We found a parasagittal organization of mossy fiber terminals in folium IXcd and observed a consistent relationship between mossy fiber organization and zebrin stripes: parasagittal clusters of mossy fiber terminals were concentrated in zebrin-immunopositive regions. We also describe the topography of projections from LM and nBOR to the inferior olive and relate these results to previous studies on the organization of climbing fibers and zebrin expression. J. Comp. Neurol. 518:175–198, 2010. © 2009 Wiley-Liss, Inc.