A-kinase anchoring protein 3 (AKAP3) is a sperm protein and its expression appears to be restricted to the testis in normal adult tissues. We investigated AKAP3 mRNA expression in 20 normal ovaries and 54 ovarian cancers of different histological types, grades and stages by reverse transcription-polymerase chain reaction (RT-PCR). The PCR products were analyzed by conventional agarose gel electrophoresis and capillary electrophoresis on a microtip device to determine the expression semiquantitatively. Little or no expression was observed in the 20 normal ovarian specimens. High AKAP3 mRNA expression was observed in 15 ovarian cancer specimens (28 %). The expression was correlated with the histological grade and clinical stage. AKAP3 mRNA was observed at a significantly higher frequency in poorly differentiated (p = 0.009) and advanced stage (III and IV, p = 0.014) tumors. No correlation was found between AKAP3 mRNA expression and other variables. In Cox multivariate analysis, AKAP3 mRNA expression was found to be a significant predictor of both overall and progression-free survival in patients with poorly differentiated tumors. © 2004 Wiley-Liss, Inc.