Thalassemia intermedia shows considerable heterogenity in phenotype and molecular basis. The aim of this study was to evaluate the prevalence and effect of different beta-globin mutations, alpha-globin defects and (G)gamma XmnI polymorphisms in Iranian patients. Forty-five Iranian patients with clinical criteria of thalassemia intermedia were studied. The molecular background of the diseases was investigated. The mean age of onset varied from 1.5 to 30 years. Only 22.2% of cases received occasional blood transfusions. The hemoglobin (Hb) level in more than half of the cases was stable (10-12 g/dL) with no need for blood transfusions. In most cases (88.9%) the Hb F level was more than 50%. Sixty-eight point nine percent of patients were homozygous for beta(0)-thalassemia (beta-thal) mutations. The positive XmnI polymorphism with the capability of enhancing Hb F production was seen in 60% of the studied chromosomes. Co-inheritance of alpha-globin gene defects was seen in 22.2% of cases. Only 8.9% of patients had beta(+) or beta(++) mutations. We concluded that the main molecular basis of the thalassemia intermedia phenotype in Iranian cases is co-inheritance of a positive XmnI polymorphism with beta-globin mutations, which can enhance the capability of Hb F production. Co-inheritance of alpha-globin defects and mild beta-globin mutations are second and third causes of thalassemia intermedia phenotypes respectively. These factors must be considered in genetic counseling, prediction of disease prognosis and treatment and prenatal diagnosis.