The present studies characterize the expression of the alpha 2A, alpha 2B and alpha 2C adrenergic receptor subtypes via in situ hybridization analysis of messenger RNA expression in the adult mouse brain, as well as the pattern of expression of alpha 2A adrenergic receptor messenger RNA at embryonic day E9.5, the earliest time for detection of the messenger RNA encoding this receptor subtype. alpha 2A adrenergic receptor messenger RNA is highly expressed in the sixth layer of the cortex and the locus coeruleus, alpha 2B adrenergic receptor messenger RNA predominantly in the thalamus and in the Purkinje layer of the cerebellum, and alpha 2C adrenergic receptor messenger RNA in the putamen caudate region of the mouse brain. Both alpha 2A and alpha 2C adrenergic receptor messenger RNA demonstrate strong expression in the amygdaloid complex, hypothalamus, olfactory system and the hippocampal formation. To develop a molecular understanding of the unique cellular expression of messenger RNA encoding the alpha 2A adrenergic receptor subtype, 2.83 kb of the upstream regulatory sequence for the alpha 2A adrenergic receptor gene was fused to the LacZ gene as a reporter gene and expression of beta-galactosidase activity was assessed in transgenic offspring. Although the spatial expression of the transgene in the adult brain often overlaps that for the endogenous alpha 2A adrenergic receptor, both ectopic expression and the absence of appropriate expression were noted; in contrast five of the six lines show temporal expression characteristic of the endogenous alpha 2A adrenergic receptor gene. The present studies provide the first characterization of messenger RNA localization for the three alpha 2 adrenergic receptor subtypes in the mouse CNS. Because the functional roles of the prazosin-sensitive alpha 2B adrenergic receptor and alpha 2C adrenergic receptor subtypes have been masked in most earlier physiological and pharmacological analyses of alpha 2 adrenergic receptor function, identifying the multiple loci alpha 2 adrenergic receptor subtype expression is an important prelude to understanding the functional roles of these three independent receptor populations in the mouse CNS. The findings in the transgenic animals indicating that approximately 3 kb of regulatory sequence has imparted faithful temporal but not spatial expression for the alpha 2A adrenergic receptor gene suggest that additional regulatory information is necessary for appropriate cell specific expression of messenger RNA for the alpha 2A adrenergic receptor subtype.