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Background Thalassemia is common in the Iranian population, and it must be considered in the differential diagnosis of the microcytic hypochromic anemia. The molecular analysis of β-thalassemia is necessary for prenatal molecular diagnosis. A-thalassemia caused by loss of function of either one of the two duplicated α-globin genes or in less frequent non deletion mutations mostly located in the α2-globin gene. Materials and Methods DNA were extracted from 100 whole blood using salting out method. The PCR was performed in two segments for entire β-globin gene and the α1 and α2-globin genes separately. Direct sequencing was carried out. The Gap-PCR was performed using published primers. Results Clinical application of DNA analysis on thalassemic patients showed 42 persons have various β-thalassemia mutations, 48 persons with αα/-α3.7 deletion and 8 persons with non deletion mutations of α1 and α2-globin genes. These mutations determined by direct sequencing of entire β-globin, α1 and α2-globin genes and Gap-PCR for detection of deletions. Thirteen different β-thalassemia alleles were identified, the most common being IVS I-5(G>C) and CAP+1 (A>C). The most α -globin mutation being αα/-α3.7 deletion. Conclusions The frequency of mutations in North-east of Iran shows that these mutations are not the same as frequent mutation in other province of Iran. Feature study could determine molecular analysis of frequent mutations, which is useful for differentiating mild from severe alleles. In addition, mutation definition in carriers should be necessary for prenatal testing and genetic counseling. [ABSTRACT FROM AUTHOR]