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Aims: To study the difference of proteins expression of epithelial cells and stroma of breast cancer patients.Methods: Formalin-fixed paraffin-embedded tissue samples from invasive ductal carcionma patients were stained by improved HE staining methods.And the neoplastic epitheilum and stroma were microdissected using laser capture microdissection and analysed by mass spectrometry.Results: Total 431 different proteins were detected by mass spectrometry and there were respectively 384 and 298 different kinds of proteins identified in epithelial cells and stroma.Among them, 251 proteins were commonly expressed in two samples, while the contents of 69 and 60 proteins in stroma were respectively higher or lower than the ones in epithelial cells.The expression level and localization of proteins identified in epithelial cells and stroma are associated with their roles in development and progression of tumor cells.Conclusions: The differential expression proteins between epithelial cells and stroma of invasive ductal carcionma patients may function as biomarkers for breast cancer screenning, diagnosis and prognosis.