Autoantibodies directed against neuronal proteins have been identified in some patients with paraneoplastic cerebellar degeneration. To identify the molecular targets for these autoantibodies, we constructed a lambda gt11 cDNA expression library from human cerebellum and screened the library with IgG from a patient with paraneoplastic cerebellar degeneration. A single clone, pCDR2, produced a fusion protein that reacted strongly with the patient's IgG. The isolated pCDR2 clone was used to identify six overlapping cDNA clones. Sequencing of the pCDR clones revealed a distinctive pattern consisting of a unit of 18 nucleotides (6 amino acids) repeated in tandem along the entire cDNA sequence. This sequence is unlike any previously described eukaryotic gene. Southern blot analysis was consistent with single-copy representation of the CDR (cerebellar degeneration-related) gene in the human and mouse genome. RNA blotting studies with normal tissues showed expression of the CDR gene to be largely restricted to brain. Expression of the CDR message was also noted in cell lines derived from cancers of neuroectodermal, kidney, and lung origin.