The molecular events leading to the development and progression of serous ovarian carcinoma are not completely understood. We performed a large scale survey for the identification of differentially expressed genes in serous ovarian carcinoma by using cDNA array analysis. Differences in gene expression between serous adenocarcinoma and benign serous adenoma, and between advanced and/or moderately or poorly differentiated and local, highly differentiated serous adenocarcinoma were assessed. The most striking difference between adenocarcinoma and benign adenoma was upregulation of RHOGDI2 in the carcinomas irrespective of the clinical tumor stage. Other changes in carcinoma were upregulation of MET and Ne-dlg, and downregulation of HGFAC, desmin, and PDGFA. The most prominent differences between advanced and local adenocarcinoma were upregulation of COL3A1, CFGR, and MET in advanced carcinoma, and downregulation of HGFAC, FZD3, and BFL1 in the same tumors. In conclusion, significant differences were found in the gene expression between benign and malignant serous ovarian tumors, and between local, highly differentiated and advanced and/or moderately or poorly differentiated serous adenocarcinomas. The differentially expressed genes may be related to the carcinogenesis and progression of the malignant growth.