Small cell lung carcinoma (SCLC) is an aggressive, highly metastatic cancer with a strong tendency for chemotherapy resistance. Identification of proteins uniquely expressed in SCLC cells, can facilitate the development of new diagnostic tools, improve immunotherapy, and deepen our understanding of the underlying mechanisms of the disease. Here we describe a comparative proteomics analysis of ten SCLC cell lines and three controls lines, while searching for proteins preferentially expressed in SCLC cells as potential disease markers. Total protein extracts were compared by two-dimensional gel electrophoresis and by two-dimensional liquid chromatography resulting in the identification of 1093 proteins, 202 of which were detected only in the SCLC cells. These include proteins of different cellular functions, including cellular proliferation and known tumor antigens. Since SCLC has a neuroendocrine origin, of major interest are the identified proteins involved in nerve and brain embryonic development. These proteins are potentially valuable as both tumor markers and as antigens for immunotherapy.