Background : Thalassemia is one of the common genetic disorders requiring lifelong blood transfusions for survival which results in accumulation of iron in the body which is toxic to many tissues, including heart. The present study was undertaken to determine the Heart Rate Variability (HRV) in beta thalassemia major patients and to compare the mean values of time domain indices of HRV in study and control group. Materials & methods : The present cross sectional study consisted of 50 normal subjects (control group) and 50 patients of beta thalassemia major (study group). HRV was recorded in both the groups with Medicaid Physiopac and HRV analysis was done using Kubois software version 2.1 Result : Time domain parameters were decreased in study group as compared to control group and the difference was statistically significant (Z test). Conclusion : The reduced levels of HRV could possibly be as a result of chronic anaemia and cardiac autonomic dysfunction secondary to iron overload cardiomyopathy due to repeated blood transfusion