The aim of this cross-sectional study is to compare endometrial flushing fluid levels of αVβ3 integrin, glycodelin and PGF2α 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 °C, αVβ3 integrin, glycodelin and PGF2α 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 αVβ3 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, PGF2α 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, αVβ3 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 PGF2α levels than those patients with myoma uteri, endometrioma and controls.