Background: Iron deficiency anemia (IDA) and thalassemia trait (TT) are the most common forms of microcytic anemia. Some discrimination indices calculated from red blood cell indices are defined and used for rapid discrimination between TT and IDA. However, there has been no study carried out in which the validity of all of the defined indices are compared in the same patient groups. Youden's index is the most reliable method by which to measure the validity of a particular technique, because it takes into account both sensitivity and specificity. Methods: We calculated eight discrimination indices (Mentzer Index, England and Fraser Index, Srivastava Index, Green and King Index, Shine and Lal Index, red blood cell (RBC) count, red blood cell distribution width and red blood cell blood distribution width index (RDWI)) in 26 patients with IDA and in 37 patients with beta TT (βTT). We determined the number of correctly identified patients by using each discrimination index. We also calculated sensitivity, specificity, positive and negative predictive value and Youden's index of each discrimination index. Results: None of the discrimination indices showed a sensitivity and specificity of 100%. Youden's indices of RBC count and RDWI were the highest with the value of 82 and 80%, respectively. Ninety percent and 92% of the patients were correctly identified with RBC and RDWI, respectively. Conclusion: Red blood cell count and RDWI are the most reliable discrimination indices in differentiation between βTT and IDA.