The aim of this cross-sectional study is to compare endometrial flushing fluid levels of alpha(V)beta(3) integrin, glycodelin and PGF2 alpha during the midluteal phase of the menstrual cycle of women with polycystic ovary syndrome (PCOS, n=20), myoma uteri (n=20) and endometrioma (n=19) with the healthy controls (n=20). After collecting samples at the midluteal phase of ovulatory volunteers and storing them at -80 degrees C, alpha(V)beta(3) integrin, glycodelin and PGF2 alpha levels were analyzed using ELISA. The mean ages of the groups were 28.90 +/- 5.45, 37.25 +/- 2.73, 32.84 +/- 6.62 and 32.15 +/- 5.18 in PCOS, myoma uteri, endometrioma and control groups, respectively. The alpha(V)beta(3) integrin level (ng/ml) was statistically significantly higher in endometrioma group (9.70 +/- 1.72, p<0.05) as compared to myoma uteri and control groups. Similarly, glycodelin level (ng/ml) was significantly higher in endometrioma group (341.04 +/- 93.32) than PCOS (p<0.01), myoma uteri (p<0.001) and healthy subjects (p<0.001). Moreover, PGF2 alpha level (350.04 +/- 464.50 ng/ml) was significantly higher in PCOS group relative to myoma uteri (p<0.001), endometrioma (p<0.05) and control (p<0.05) groups. In conclusion, alpha(V)beta(3) integrin level was significantly higher in endometrioma subjects than those with myoma uteri and control groups; glycodelin level was significantly higher in endometrioma group than other three groups, and lastly, PCOS patients had significantly higher PGF2 alpha levels than those patients with myoma uteri, endometrioma and controls.