The aim of this study was to develop an immunohistochemical (IHC) method for calbindin D-28 (CB-28) and microtubule-associated protein-2 (MAP-2) and evaluate their expression as markers in the detection, characterisation and grading of unexpected cerebellar toxicity in the rat. High power examination of H&E-stained brain sections of treated rats 2 days following a single oral dose of a novel compound revealed irregular vacuolation of the molecular layer and Purkinje cell degeneration. Animals killed after 14 days recovery showed Purkinje cell degeneration but vacuolation of the molecular layer was absent. In control animals, CB-28 and MAP-2 expression was high in Purkinje cell dendrites and cell bodies in the molecular layer. In treated animals, low power examination revealed loss of CB-28 and MAP-2 expression in degenerating neurons arranged in parasagittal stripes within the vermis. This is the first description of successful use of these two markers in a regulatory toxicity study using FFPE brain. In particular, CB-28 provides a sensitive method for characterising CNS toxicity which can be detected at low power enabling easier detection, screening and grading of neurotoxicity.