The characteristics that distinguish the different neuronal cell types of an organism are believed to be primarily determined by unique patterns of cellular gene expression. The identification of cell-type specific molecules should therefore provide a good basis for understanding the biology of specific neuron types. In this paper, we describe the isolation of cDNA clones corresponding to mRNA uniquely expressed by Purkinje cells in mature mouse cerebellum. Three cDNA clones were selected from a library of normal mouse cerebellar cDNA by virtue of their failure to hybridize to mRNA sequences from the cerebella of Purkinje cell degeneration (pcd) mice. The cDNA clones were shown by in situ and Northern hybridization to correspond with mRNA present in Purkinje cells but absent or at low levels in other cell types of the cerebellum. By sequence analysis, clone PCD29 was determined to encode the calcium-binding protein calbindin-D28K. Clones PCD5 and PCD6 encode previously undescribed proteins of 99 and greater than 500 amino acids, respectively. All 3 PCD clones hybridized to mouse mRNA from sources other than cerebellum; clone PCD5 was found to have the most restricted expression, as it hybridized only to mRNA from cerebellum and eye. To define potential correlations between the PCD clones and mutations in the mouse genome known to affect Purkinje cells, clones PCD5, PCD6, and PCD29 were localized to mouse chromosomes 8, 6, and 4, respectively.