<p>Background: Endometriosis is an estrogen-dependent chronic progressive gynecological disease that affects around 10% of women of reproductive age. A recent study shows that brain-derived neurotrophic factor (BDNF) has the potential as a clinical marker in the diagnosis of endometriosis. We aimed to determine whether BDNF levels are correlated with pain scores associated with endometriosis.<br /> Methods: Fifty women who underwent laparoscopy surgery at Dr. Soetomo General Hospital and Dr. Ramelan Navy Hospital were prospectively recruited from October 2017 until August 2018. A blood sample was obtained before surgery and BDNF was measured using the Human BDNF Quantakine&reg;️ kit. The relationship of BDNF levels in serum with the diseases&#39;s level of pain and stages was compared between cases and controls. BDNF validity as an endometriosis diagnosis biomarker was assessed using receiver operating characteristic (ROC) analysis.<br /> Results: Serum concentrations of BDNF were significantly greater in women with endometriosis (30.42&plusmn;7.41 <em>pg/ml</em>), compared to controls (25.66&plusmn;3.30 <em>pg/ml</em>). Serum concentrations of BDNF were moderately correlated with the patient&rsquo;s reported pain scores (r=0.44, p=0.01). Receiver operating characteristic curve analysis confirmed the potential of BDNF in the diagnosis of endometriosis. Using a cut-off value of 27.06 <em>pg/ml</em>, the sensitivity and specificity were reported to be 66.7% and 64.3%, respectively.<br /> Conclusion: BDNF serum levels in endometriosis women are significantly higher than in women without the disorder. BDNF serum level seems to have low accuracy and predictive value as a diagnostic marker for endometriosis. However, there was a moderate relationship between BDNF serum level and the degree of pain.</p>