With the steadily improving resolution of novel small-animal single photon emission computed tomography (SPECT) and positron emission tomography devices, highly detailed phantoms are required for testing and optimizing these systems. We present a three-dimensional (3-D) digital and physical phantom pair to represent, e.g., cerebral blood flow, glucose metabolism, or neuroreceptor binding in small regions of the rat brain. The anatomical structures are based on digital photographs of the uncut part of a rat brain cryosection block. The photographs have been segmented into ventricles and gray and white matter and have been stacked afterwards. In the resulting voxelized digital phantom, tracer concentration in gray and white matter can be scaled independently. This is of relevance since, e.g., cerebral blood flow or metabolism are much higher in gray than in white matter. The physical phantom is based on the digital phantom and has been manufactured out of hardened polymer using rapid prototyping, a process in which complicated 3-D objects can be built up layer by layer. X-ray computed tomography and high-resolution SPECT images of the physical phantom are compared with the digital phantom. The detailed physical phantom can be filled bubble-free. Excellent correspondence is shown between details in the digital and physical phantom. Therefore, this newly developed brain phantom will enable the optimization of high-resolution imaging for recovery of complex shaped molecular distributions.