To identify genes involved in the development or progression of ovarian cancer, we analyzed gene expression profiles of nine ovarian tumors using a DNA microarray consisting of 9121 genes. Comparison of expression patterns between carcinomas and the corresponding normal ovarian tissues enabled us to identify 55 genes that were commonly up-regulated and 48 genes that were down-regulated in the cancer specimens. When the five serous adenocarcinomas were analyzed separately from the four mucinous adenocarcinomas, we identified 115 genes that were expressed differently between the two types of tumor. Investigation of these genes should help to disclose the molecular mechanism(s) of ovarian carcinogenesis and define molecular separation of the two most common histological types of ovarian cancer.