Ca2+/calmodulin-dependent protein kinase II (CaM kinase II) consisting of alpha and beta isoforms is highly expressed in the central nervous system and is implicated in the regulation of various Ca2+-dependent physiological processes. We investigated the immunohistochemical distribution of the alpha and beta isoforms of this enzyme in the rat retina, using highly specific monoclonal antibodies which recognize each isoform. Immunoblotting revealed that not only the alpha but also the beta isoform of CaM kinase II were expressed in the retina. The immunohistochemical study showed that highly alpha-immunoreactive products were localized in amacrine cells in the inner nuclear layer and displaced amacrine cells and ganglion cells in the ganglion cell layer. In addition, two well-defined bands within the inner plexiform layer were densely stained with the anti-alpha antibody. By contrast, immunoreactivity against the anti-beta antibody was very weak in the same neuronal components of the retina. beta-Immunoreactive products were homogeneously distributed throughout the inner plexiform layer and no well-defined bands were detected in this layer. Glial cells such as Muller cells were immunoreactive neither to alpha nor beta antibody. A possible co-existence of choline acetyl transferase (ChAT) within CaM kinase II alpha-immunopositive neurons was examined by evaluating adjacent sections stained with anti-CaM kinase II alpha antibody and anti-ChAT antibody, respectively. The distribution of CaM kinase II alpha immunoreactivity in the rat retina was remarkably similar to that of ChAT immunoreactivity. About 32% of total ChAT-immunopositive neurons in the inner nuclear layer contained the CaM kinase II alpha isoform, whereas only an occasional co-existence of both enzymes was observed in the ganglion cell layer. The present immunoblot and immunohistochemical study elucidated that not only alpha but also beta isoforms of CaM kinase II beta were expressed and this enzyme may participate in the cholinergic system in the rat retina.