The kidney has a complicated structure consisting of a number of different segments, each of which plays different roles orchestrating for the maintenance of body fluid and electrolyte balance. Functional unit is a nephron composed of glomerulus and the following tubular segments. In a glomerulus, where plasma filtration occurs, there are three cell types, including endothelial cells, epithelial cells (also called podocytes) and mesangeal cells, whereas the tubules are divided into functionally and anatomically distinct segments, namely proximal tubule, loop of Henle, distal tubule, and the cortical and medullary collecting duct, generating urine through reabsorption and secretion via tubular epithelia. Renal diseases are caused by functional or organic defect of various causes in any part or a whole of renal tissues, nephron segments, cells, or even molecule such as transporter in the tubules; thus, selective approach will be required to clarify the pathophysiology. In animal models, such a selective renal segment collection is feasible; thus, a number of basic proteomic research studies have been conducted in the last decade. In human analysis, the target tissues are mainly obtained by renal biopsy and sometimes by autopsy. Therefore, the major problem in human kidney proteome analysis may be that renal biopsy samples contain only small parts of the kidney yielding a tiny and usually insufficient amount of proteins [7]. However, recent progress in laser captured microdissection (LCM) and isolating techniques using FACS has made it possible to analyze the small sections or cells selectively from biopsy samples or selective tissues (see below). The sensitivities of protein identification have been improving but still not satisfactory, thus, more sensitive protein identification and analyzing techniques should be developed.