In addition to the large alpha subunits that conduct selective ion currents, many native voltage-gated ion channels contain associated proteins which modulate the channel activity. Recently, a beta subunit of the large-conductance calcium-activated K+ (BK) channel has been cloned and functionally characterized. In this report, we studied the tissue distribution of the alpha and beta subunits of rat BK channels by nuclease protection analyses and in situ hybridization. BK alpha mRNA is widely distributed but is especially enriched in the brain. In the adult brain, BK alpha expression is robust and widespread throughout all areas of the neo-, olfactory and hippocampal cortices, habenula and cerebellum. Other prominent sites of BK alpha expression include thalamus and amygdala. In marked contrast to the expression pattern of BK alpha mRNA, the expression of BK beta mRNA is relatively low and preferentially in the periphery. In rat brains, BK beta mRNA occurs only in a few discrete populations of neurons that also express BK alpha messages. These results indicate that the major type of BK channels in the brain, unlike the alpha beta channel type in aortic and tracheal smooth muscle, is devoid of the beta subunit. These observations provide a structural basis for the BK channel diversity observed in a variety of tissues.