Histaminergic H3 receptors modulate the release of neurotransmitters within the CNS and periphery. Ligands for these receptors have potential clinical utility in a variety of disease states. However, the pharmacological characteristics of these receptors have been enigmatic for more than a decade because of the diversity of pharmacological effects observed with the limited number of heretofore-available compounds. Recent cloning of the H3 receptor has revealed interspecies differences in the protein sequences in key regions, the existence of splice variants that differ in composition between species, and potential differences in signal transduction processes between either different tissues and/or species. This review attempts to summarize these findings within the context of the molecular biological and pharmacological data accumulated to date. Also, we suggest a nomenclature strategy to reduce potential confusion that has arisen from different naming systems used by various investigators. While some facets of this genetic and pharmacological diversity help to rationalize various aspects of H3 receptor heterogeneity, there remains an insufficient repertoire of selective ligands, assays, or other measures to completely resolve all components of this diversity. The promise of newly available tools to further explore H3 receptor function may provide the insight to bring the promised clinical potential of H3 receptor ligands to realization.