The expression of 12 different classic cadherins and δ-protocadherins was mapped in consecutive series of sections through the basal ganglia of the postnatal and adult mouse by in situ hybridization. A particular focus was the caudoputamen, which consists of patches (striosomes) and a surrounding matrix that is histologically uniform. The different areas within the caudoputamen are connected specifically to other parts of the basal ganglia and to other brain regions, for example, the substantia nigra. The molecules regulating the morphogenesis and functional connectivity of the basal ganglia are largely unknown. Previous studies suggested that cadherins, a large family of adhesion molecules, are involved in basal ganglia development. In the present work, we study the expression of 12 cadherins and show that the patch and matrix compartments of the caudoputamen express the cadherins differentially, although partial overlap is observed. Moreover, the cadherins are expressed in multiple and diverse gradients within the caudoputamen and other parts of the basal ganglia. The persistence of the expression patterns in the adult basal ganglia suggests the possibility that cadherins also play a role at adult stages. Our results suggest that cadherins provide a code of potentially adhesive cues that specify not only patch and matrix compartments but also multiple molecular gradients within the basal ganglia. This code may relate to patterns of connectivity. J. Comp. Neurol. 508:511–528, 2008. © 2008 Wiley-Liss, Inc.