In clinical neuroscience as well as in many other clinical disciplines, the completion of the human genome project offers a new possibility to identify and localize the products of the genes, the proteins. Nuclear proteins are synthesized in the cytoplasm and imported into the nucleus by multiple pathways. The mechanisms by which nuclear accumulation of different molecular species occur are unclear but it is apparent that changes in the cellular and molecular events associated with the accumulation of nuclear proteins sometimes precedes transformation of cells into diseased states. The significance of the accumulation and the operation of nuclear proteins remain to be elucidated in detail. Such knowledge will play a key role in the understanding of the regulation of transcription and its disturbances in several of our most devastating diseases. In this paper we present a strategy to identify nuclear associated proteins in small samples by using two-dimensional electrophoresis and mass spectrometry. We have used human blood lymphocytes as a model, but the method should be rather general for any kind of tissue. Twenty two proteins were randomly chosen, and of these 18 proteins were identified by database searching of mass spectrometric data, obtained from in-gel tryptic digests of the spots. Thirteen proteins recently described with nuclear localization and function were identified, and five proteins; calgranulin B, glyceraldehyde-3-phosphate dehydrogenase (G3P2), a TATA-binding protein (ATBP), tubulin beta chain and moesin were also identified as being nuclear associated. The presented data clearly shows of the great role of two-dimensional gel electrophoresis and modern mass spectrometry in the excavation of the protein patterns on the subcellular level, and the ability to use small samples well suited for clinical screening.