Kalirin is a neuron-specific GDP/GTP exchange factor for Rho subfamily GTP-binding proteins. The major Kalirin transcripts in adult rat brain were identified. Most include a Sec14p-like putative lipid-binding motif followed by nine spectrin-like repeats and a Dbl homology/pleckstrin homology (DH-PH) domain. Kalirin proteins with four different NH(2) termini are generated through the use of five different 5'-ends; three of the proteins differ only at the extreme NH(2) terminus, and one is truncated because translation is initiated at a methionine in the 5th spectrin repeat. Four different 3'-ends yield Kalirin proteins with additional functional domains. Kalirin-7 (7-kilobase pair mRNA) terminates with a PDZ-binding motif, which in Kalirin-8 is replaced by an SH3 domain. Kalirin-9 contains another pair of DH-PH and SH3 domains. Kalirin-12 additionally encodes a putative Ser/Thr protein kinase. Antisera specific for different COOH termini established Kalirin-7 as the most abundant in cortex, with significant amounts of Kalirin-9 and Kalirin-12; Kalirin-7 was less prevalent in cerebellum and olfactory bulb. Kalirin proteins lacking the Sec14p-like domain and first four spectrin-like repeats were much less prevalent. Form-specific antisera demonstrated that different forms of Kalirin were localized to distinct subcellular regions of cultured neurons. Members of the family of Kalirin proteins may subserve different functions at these different locations.