Abstract Electrophysiological mapping of the rat cerebellar cortex has revealed an elaborate functional somatotopy that tract tracing procedures have shown to correlate with specific patterns of afferent and efferent connectivity that encompass the cerebellum as a whole. In contrast, most anatomical and biochemical procedures suggest that the cerebellar cortex is remarkably uniform. To unmask covert molecular heterogeneity underlying the functional map, it is appropriate to use monoclonal antibody technology to search for antigenic epitopes whose cerebellar distribution reflects or encodes the positional information. Given that no preconditions can be set on the biochemical nature of the putative epitopes, a shotgun approach to immunization and screening is required. The construction of monoclonal antibodies and screening for specificities that reveal positional information is discussed with examples from an anti-cerebellar antibody library.