We cloned the full length guinea pig H3 receptor cDNA using RT-PCR amplification with primers from the human receptor and templates from brain areas. Evidence was obtained for two isoforms, designated H3L and H3S, differing by a 30 amino acid stretch within the third cytosolic loop, presumably generated by alternative splicing. In situ hybridization using a selective cRNA probe showed the gene transcripts to be highly expressed in discrete neuronal populations, e.g. pyramidal cells in the cerebral cortex or cerebellar Purkinje cells, in some instances already known to express other histamine receptor subtypes.