Two-dimensional differential in-gel electrophoresis technology (2D DIGE) technique is highly useful for differential analysis of protein spots in two-dimensional differential gels. Utilizing this technique, we attempted to search for diabetes-related drug targets and biomarkers. In human hepatoma cell line, HepG2, we analyzed secretome in the presence or absence of a Liver X receptor agonist, TO-901317, and identified one of the up-regulated proteins in response to LXR activation as apolipoprotein E. We also evaluated nuclear proteome of cultured cells overexpressing insulin receptor substrate proteins, in which insulin-stimulated cell cycle progression is differentially regulated, and the gel pattern indicated that insulin-induced phosphorylation of a nuclear protein may be impaired in cells overexpressing cell cycle-suppressive insulin receptor substrate-3. In addition, to search for urinary markers of diabetic nephropathy using 2D DIGE, we analyzed urine samples in which most abundant proteins were removed by immunoaffinity depletion. These findings indicate that the 2D DIGE-based approach is useful for the discovery of disease-specific drug targets and diagnostic biomarkers.