Differentiation of epithelial cells involves the assembly of polarized membrane transport machineries necessary for the generation and maintenance of the apical and basolateral membrane domains characteristic of this cell type. We have analyzed the expression patterns of vesicle-docking proteins of the syntaxin family in mouse kidney, focusing on syntaxin 3 and its interaction partner, the Sec1-related Munc-18-2.Expression patterns were studied by in situ hybridization and immunocytochemistry and the complex formation of syntaxin 3 and Munc-18-2 by coimmunoprecipitation and Western blotting.We have previously shown by in situ hybridization that Munc-18-2 is present in the proximal tubules and collecting ducts of embryonic day 17 mouse kidney. We compared this with the expression patterns of syntaxin 1A, 2, 3, 4, and 5, and found that syntaxin 3 was enriched in the same epithelial structures in which Munc-18-2 was abundant. By immunocytochemistry, the two proteins colocalized at the apical plasma membrane of proximal tubule and collecting duct epithelial cells, and they were shown to form a physical complex in the kidney. The expression of both proteins was up-regulated during kidney development. The most prominent changes in expression levels coincided with the differentiation of proximal tubules, suggesting a role in the generation of the highly active reabsorption machinery characterizing this segment of the nephron.The results show that Munc-18-2 and syntaxin 3 form a complex in vivo and suggest that they participate in epithelial cell differentiation and targeted vesicle transport processes in the developing kidney.