This study examined the spatial organization of corticotropin-releasing factor (CRF) immunopositive climbing fibers in the mouse cerebellum by whole mount immunohistochemistry. A striking pattern of parasagittal stripes of CRF staining was revealed. Cryosections of whole mount CRF stained cerebellum showed that anti-CRF immunostaining is restricted to climbing fibers in the molecular layer and does not penetrate deeper into the granular layer. The array of CRF stripes was reminiscent of zebrin II immunopositive Purkinje cell stripes in the anterior vermis and the hemispherical lobules. However, a direct comparison of the two distributions showed that the CRF-defined parasagittal stripes and transverse zones in the posterior vermis are different from those defined by the expression of zebrin II: in particular, CRF immunostaining revealed a transverse boundary between lobules VIb and VII and the presence of four CRF-immunopositive climbing fiber stripes in lobule VIII. Furthermore, an array of CRF stripes was seen in lobule X, the flocculus and the paraflocculus, despite uniform zebrin II expression in these areas. In these cases some, but not all, CRF-immunopositive stripes shared boundaries with Purkinje cell stripes that were visualized by the expression of heat shock protein 25. The results reveal a reproducible pattern of CRF-immunopositive climbing fiber innervation in the mouse cerebellum that bears a complex relationship to the stripes delineated by Purkinje cell compartmentation antigens.