Introduction: Thalassemia is an inherited autosomal recessive blood disease that originated in the Mediterranean region. In thalassemia the genetic defect, which could be either mutation or deletion, results in reduced rate of synthesis or no synthesis of one of the globin chains that make up hemoglobin. This can cause the formation of abnormal hemoglobin molecules, thus causing anemia. The basic aim of this study was to identify a suitable molecular approach for prevention of thalassaemia in Mashhad. Material and methods: DNA was extracted from peripheral blood and the whole beta-globin and the entire alpha1 and 2 globin genes were amplified and DNA sequenced. The seven common deletion mutations for apha-globin genes were investigated. Results: Molecular basis of thalassaemia was investigated in 88 mutant alleles. Eighty different mutations were found including one novel allele. Coincidental a-thalassaemia was found in 16% of cases of thalassaemia. Consanguineous marriage and recessive disorders were studied. In 44 couples studied 70% were consanguineous and only 30% were completely unrelated. Discussion: Over 98% of the diagnoses were done by direct mutation analysis. A multiplex polymerase chain reaction for mutation analysis was used and significantly reduced the total cost and time required for prenatal diagnosis. This pilot study appears to have identified a suitable approach for prevention of thalassaemia in Mashhad.