Background: Basal Cell Carcinoma (BCC) is a type of non-melanoma skin cancer. Alteration in gene expression is the important event that happens in cancer cell. Detection of this event is possible by proteomics techniques. Methods: Normal and tumor tissues were taken from BCC patient. Total proteins were purified by standard methods, and proteins were separated by two-dimensional electrophoresis (2DE). Mass spectrometry (MS-MALDI method) was used as a powerful instrument for protein identification. Results: Eighty seven spots of protein were detected in 2DE gels out of which, 76 spots had different expression in normal and cancer gel images. Comparison with the data base showed 11 proteins. Nine spots had no association with BCC, but expression of ceruloplasmin and C3b were decreased and increased respectively in cancer tissues, compared to normal cell. The mass spectrometry results were aldolase C, Prx-cis and VDAC. Conclusion: These recognized proteins, either with increased or decreased expression in cancer tissue, might be considered as new biomarkers in BCC patients.