The molecular genesis of a tumor is a multi-step and complex process in which many factors are involved such as oncogenes, tumor suppressor genes and MHC-I etc. Metastasis is the essential character causing mortality from such tumors and little is currently known about mechanisms underlying cancer metastasis. As a step toward understanding the complex differences between high metastatic and low metastatic cells, metastasis-associated gene expression patterns and proteomes were separated and identified by suppression subtraction hybridization and comparative proteomics analysis between high metastatic cell AccM and low metastatic cell Acc2. Although extensive similarity was noted between the expression profiles of the two cell lines, twenty-eight genes highly expressed were obtained in tester, low metastatic cells, compared with their low expression in driver, high metastatic cells while six genes in reverse hybridization. These function of genes are related to cell proliferation, differentiation or cell metabolism while several novel EST sequences which function are unknown. Two novel genes were ACC metastasis-associated RNH ACC metastasis-associated suspected protein. Meanwhile, ten proteins were randomly selected which are expressed different qualitatively or quantitatively and identified by mass fingerprinting (MALDI-TOF-MS). These proteins are stratifin, symplekin, B7, TPMsk1 tropomyosin isoforms, serologically defined breast cancer antigen NY-BR-20 etc. Intriguingly, most identified candidate proteins have been shown to be somehow associated with distinct aspects of tumor metastasis such as cell communication protein, motility, adhesion, invasion and tumor immunity associated protein, etc. These results suggest that attaining the ability to metastasize is related to the changed expression of these genes or protein. These data provide insight into the extent of expression differences underlying metastasis-related genes that may prove useful as diagnostic or prognostic markers.