Although the discrimination between β-thalassemia trait (βTT) and Iron deficiency anemia (IDA) is important clinically, but it is challenging and normally difficult; so if a patient with IDA is diagnosed as βTT, then it is deprived of iron therapy. This study purpose was to evaluate the 26 different discriminating indices diagnostic function in patients with microcytic anemia by using accuracy measures, and also recommending two distinct new discriminating indices as well. In this study, 907 patients were enrolled with the ages over 18-year-old with either βTT or IDA. Twenty-six discrimination indices diagnostic performance presented in earlier studies, and two new indices were introduced in this study (CRUISE index and index26) in order to evaluate the differential between βTT and IDA by using accuracy measures. 537 (59%) patients with βTT (299 (56%) women, and 238 (44%) men), and also 370 (41%) patients with IDA (293 (79%) women, and 77 (21%) men) were participated in this study for evaluating the 28 discrimination indices diagnostic performance. Two new introduced indices (CRUISE index and index26) have better performance than some discrimination indices. Indices with the amount of AUC higher than 0.8 had very appropriate diagnostic accuracy in discrimination between βTT and IDA, and also CRUISE index has good diagnostic accuracy, too. The present study was also the first cluster analysis application in order to identify the homogeneous subgroups of different indices with similar diagnostic function. In addition, new indices that offered in this study have presented a relatively closed diagnostic performance by using cluster analysis for the different indices described in earlier studies. Thus, we suggest the using of cluster analysis in order to determine differential indices with similar diagnostic performances.