The aim of this study was to globally characterize the expression profile of superficial transitional cell carcinoma using shotgun proteome strategy and to discuss the biomarker panel identified from urine. We identified 440 commonly expressed proteins from four samples of superficial transitional cell carcinoma using laser capture microdissection coupled with two-dimensional liquid chromatography tandem mass spectrometry. The identified proteins were further analyzed using bioinformatics tools and compared with the published literature. Compared with the entire list of the International Protein Index, there were 41/22 Gene ontology (GO) terms found to be enriched/depleted within the biological process annotation. GO biological process enrichment/depletion analysis was consistent with the results of urine proteome analysis. Proteins classified under the terms cell adhesion, cell proliferation and cell differentiation are good candidate biomarkers for cancer detection from urine. In conclusion, the present study identified an extensive expression profile in superficial transitional cell carcinoma of the bladder, providing information for the understanding of cancer cell biology and the discovery of a biomarker panel from urine.