Diabetes mellitus (DM) is currently one of the principal causes of end stage renal disease (ESRD). Approximately 40% of all diabetic patients eventually develop diabetic nephropathy (DN). The complexity of diabetes and its complications require a broad-based, unbiased, scientific approach, such as proteomics, in order to understand the progression of DN. Proteomic techniques have been applied extensively to explore the complexity of the mechanisms associated with DN, and to identify novel biomarkers and therapeutic targets. This review provides insights into how proteomics can be applied to DN, and how experimental data can be linked to clinical applications. In addition, recent proteome studies of DN are summarized. The rapid rate of development of the relevant technologies, along with the combination of classic physiological and biochemical techniques with proteomics will facilitate new discoveries.