Iron overload is a well-documented complication in thalassemia intermedia. Moreover, it is seen that the number of blood transfusions received does not correlate with the degree of overload. Since, HFE gene is associated with iron overload; the present study was conducted in an attempt to evaluate its role in thalassemia intermedia. The subjects were consecutive thalassemia intermedia cases attending the Hematology outpatient clinic. Controls were healthy hospital staff with negative family history of hemolytic anemia or liver disease. The molecular analysis for HFE mutations H63D and C282Y were done with primers described earlier. ELISA was used to measure serum ferritin. Sixty-three patients of thalassemia intermedia including 48 beta-homozygous/heterozygous thalassemia intermedia and 15 HbE-beta-thalassemia were studied. Six (12.5%) of the former and two (13.3%) of the latter were heterozygous for H63D; one of which, a 51-year old male also had clinical features of hemochromatosis. In healthy controls, prevalence of H63D heterozygosity was 7.5% (6/80). An interesting feature observed was that though the age and transfusions taken were similar in both groups, the serum ferritin greater than 500 ng/dl were observed in all patients (100%) with HFE mutation whereas it was seen in 12/42 (28.6 %) of patients without the mutation (p = 0.002). Thus, it is concluded that thalassemia intermedia patients with co-existent HFE mutation have a higher likelihood of developing iron overload and may require early iron chelation.