Matrix metalloproteinase-1 (MMP-1), MMP-2, and MMP-9 expression with real-time quantitative polymerase chain reaction were analyzed in endometriotic and nonendometriotic ovarian cysts. Although MMP-1 was not detected, MMP-9 and MMP-2 were expressed in all of the cysts. In particular, in five of six nonendometriotic cysts (83.3%) MMP-2 expression was higher than in endometriotic cysts. These data may represent new molecular elements helpful in differential diagnosis of endometriotic lesions.