For analysis of in vivo dopamine receptor binding in the rat brain by positron emission tomography (PET), a convenient method to obtain precise anatomical registration for striatum and cerebellum on the PET image was developed. On the PET measurements, a control, an anesthetized rat was positioned in a stereotaxic holder so that the horizontal plane of the PET image would be parallel to the horizontal plane of the brain atlas. After the positioning, [11C]raclopride was intravenously injected into the rats and scanned to obtain PET images of dopamine D2 receptor in the brain. The striatum was bilaterally identified in the obtained PET image. The atlas-based regions of interest (ROIs) of the whole brain were preliminarily created according to the atlas, and were superimposed on an early phase PET image. The early phase PET image was compatible to the whole brain ROI in the atlas, which enabled determination of striatal and cerebellar ROI difficult to determine by the PET image alone. Using the cerebellar radioactivity as a reference input function, rate constants between the free/nonspecific compartment and the receptor bound compartment (k3 and k4) were calculated by a two-parameter compartment model, and the binding potential (k3/k4) was estimated. The binding potential and its coefficients of variation were 1.56+/-0.30, 19.3% in Wistar rats, 1.05+/-0.14, 13.4% in Sprague-Dawley (SD) rats, and 1.29+/-0.07, 5.2% in Fischer F344 rats, in which binding potential in Wistar rats was significantly higher than that in SD rats. This method is objective and convenient in routine use for PET studies in rats, regardless of differences in the rat strains.