The progress in understanding visual signal transduction in vertebrate photoreceptors, arguably the best studied G protein-mediated signal transduction cascade in modern biology, was facilitated by the unique anatomy of rod photoreceptors. Held only by thin connected cilia, rod outer segments can be readily separated from the rest of the retina simply by shaking, and then purified by gradient centrifugation. The availability of such an efficient procedure of rod outer segment purification not only previously facilitated the identification of many principal visual signaling proteins located in this cellular compartment, but it is also currently being exploited in proteomics studies. In this paper, we describe a simple and inexpensive technique that allows for the quantitative analysis of protein expression within different subcellular compartments of photoreceptors, and could also be used for studying protein expression in the secondary retinal neurons. This technique is based on the Western blot analysis of the protein content of serial sections obtained by tangential sectioning of flat-mounted frozen retinas from mouse and rat, and it could serve as a way to validate proteomic data, similar to the way the quantitative RT-PCR technique is used for validation of gene-microarray data. To demonstrate the utility of this technique, we have determined the expression profiles in normal mouse retina of several signaling, energy-producing, and chaperone proteins, which were recently identified in bovine rod photoreceptors by mass spectrometry.