A general pattern of organization of the forebrain shared by amphibians, mainly anurans, and amniotes has been proposed considering the relative topography of the territories, their connectivity, and their neurochemistry. These criteria were needed because the amphibians possess limited cell migration from the ventricle that precludes a parcellation into circumscribed nuclei. In the present study we have tested the identity of most newly described forebrain territories in anurans and urodeles with regard to their content in calbindin-D28k (CB) and calretinin (CR). By means of immunohistochemistry, these proteins were demonstrated to be particularly abundant and specifically distributed in the amphibian forebrain and were extremely useful markers for delineating nuclear boundaries otherwise indistinguishable. In the telencephalon, labeled cells in the pallium allowed the identification of particular regions with marked differences between anurans and urodeles, whereas the subpallium showed more conservative patterns of distribution. In particular, the components of the amygdaloid complex and the basal ganglia were distinctly labeled. The distribution in the nonevaginated secondary prosencephalon and diencephalon showed abundant common features between anurans and urodeles, highlighted using the prosomeric model for the comparison. In the pretectum, thalamus, and prethalamus of urodeles, the CB and CR staining was particularly suitable for the identification of diverse structures within the simple periventricular gray layer. However, the analysis across species also revealed a considerable degree of heterogeneity, even within comparatively well-defined neuronal populations. Therefore, the content of a particular calcium binding protein in a neuronal group is not a fully reliable criterion for considering homologies. J. Comp. Neurol. 511:187–220, 2008. © 2008 Wiley-Liss, Inc.