Ovarian cancer is the most malignant gynecologic neoplasm. Although new chemotherapeutic agents have improved patients' 5-year survival rate, the overall mortality of ovarian cancer has remained largely unchanged in the past several decades. The main reason for the lack of success in effectively treating ovarian cancer is our limited understanding of its etiology and the very few molecular diagnostic markers and therapeutic targets known so far. Identification and characterization of ovarian cancer-associated genes are fundamental for unveiling the pathogenesis of its initiation and progression, especially the development of recurrent diseases. As there are a vast number of genes for which molecular genetic changes and aberrant gene expression have been reported in ovarian cancer, this review will only focus on summarizing those exemplified genes that have been demonstrated to have biological functions in promoting ovarian cancer development and potential clinical significance. The genes to be discussed include nuclear proteins (Notch3, HBXAP [Rsf-1], NAC1 and NFkappaB), cytoplasmic proteins (fatty acid synthase and apolipoprotein E) and cell surface/secretory proteins (mucin-4, mesothelin, claudin, HLA-G, kallikrein and folate receptor and osteopontin). Since the study of ovarian cancer-associated genes is complicated by several factors unique to ovarian cancer, we will also present our views on the limitations and challenges of current ovarian cancer research.