Objective: Brain-derived neurotrophic factor (BDNF) and high sensitive C-reactive protein (hs-CRP) have been reported to play roles in depression and bipolar disorder (BD). However, the probable discriminatory properties of these biologic markers are less investigated. We aimed to assess the serum BDNF and hs-CRP levels among Iranian patients with major depressive disorder (MDD) and BD during a depressive episode and investigate the optimum cut-off point for differential diagnosis of BD and MDD. Methods: We recruited 30 patients with MDD, 30 with BD in depressive mood and 30 healthy comparators. Blood sample was taken from each participant to measure BDNF and hs-CRP levels. We also used receiver operating characteristic (ROC) curve analysis to find an optimal cut-off point for differentiating MDD from BD according to pre-defined variables. Results: The mean age of total study population was 37.3 ± 5.0 years (males: 49%). BDNF was significantly lower in patients with BD, followed by MDD subjects and healthy controls 541.0 ± 601.0 pg/ml vs. 809.5 ± 433.3 pg/ml vs. 1,482.1 ± 519.8, respectively, p ＜ 0.001). The area under curve of ROC curve analysis for BD versus MDD was 0.704 (95% confidence interval: 0.564−0.844, p = 0.007). We also found that the BDNF cut-off value of 504 could appropriately distinguished BD from MDD (sensitivity: 73%, specificity: 70%). No significant association were identified in terms of hs-CRP levels. Conclusion Patients suffering from BD had lowest BDNF levels compared to MDD or healthy adults and this biomarker could play a practical role differentiating MDD from BD. Several studies are required confirming our outcomes.