Background: Endometriosis is a common devastating gynecological disease with severe complications. Researches on noninvasive diagnostic tests with acceptable accuracy are still ongoing. The purpose of the present study was to evaluate the diagnostic value of serum Galectin-9 (Gal-9) level in comparison with laparoscopic results in endometriosis patients. Methods: Sixty-one patients, referred to Booali, Rasool-e-Akram, and Pars Hospitals affiliated to Islamic Azad University of Medical Sciences, were recruited. Patients laparoscopically diagnosed with endometriosis were assigned to the case (n=32) and who diagnosed with other diseases were assigned to the control group (n=29). In general, 56 patients (30 in case and 26 in control group) completed the study. The serum level of Galectin-9 was measured using ELISA method before laparoscopy and was compared between the groups. Next, categorical variables were compared using Chi square and quantitative variables using independent samples t-test or Mann-Whitney U test. The Gal-9 cut-off was calculated using the Youden’s index and ROC curve; then, sensitivity, specificity, positive and negative predictive value, and positive and negative likelihood ratio of Gal-9 were reported. The p<0.05 were considered statistically significant. Results: Mean serum level of Galectin-9 was 669.3±416.50 pg/ml in the case group and 265.42±492.30 pg/ml in the control group (p=0.001). Considering a cut-off value of 138 pg/ml, Galectin-9 had a sensitivity of 100% and specificity of 88.46% for diagnosis of endometriosis (p<0.001). Conclusion: Galectin-9 measurement is helpful in diagnosis of endometriosis. Future studies are recommended for investigating the generalizability of these results.