Background: Splenectomy is a common treatment for beta thalassemia. It not only eliminates many complications by reducing the need for blood transfusion, but also causes new complications that threaten the patients' health. The aim of this study was to determine if splenectomy could alter the lipid profile and glucose metabolism in beta thalassemia major patients. Methods: In this case-control study, 41 splenectomized and 42 non-splenectomized eligible beta thalassemia patients were selected from Zafar Thalassemia Clinic, Tehran, Iran. Anthropometric, demographic, and biochemical data were collected using standard methods. Physical activity and food intake were measured using International Physical Activity Questionnaire (IPAQ) and food frequency questionnaires (FFQ), respectively. Results: Demographic characteristics and dietary intake were not significantly different between the two groups. However, triglyceride (TG), total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), very low density lipoprotein cholesterol (VLDL-C), TC/HDL-C, LDL-C/TG, and LDL-C/HDL-C ratios were significantly higher, but HDL-C was significantly lower in splenectomized patients (P < 0.05). Furthermore, fasting blood glucose (P < 0.39) and oral glucose tolerance test (P < 0.53) did not significantly differ between the two groups. Conclusions: Reduced activity of the reticuloendothelial system and reduced removal of cholesterol might be the reason for higher plasma lipid profile and greater risk of cardiovascular diseases in splenectomized patients. On the other hand, glucose metabolism was not affected by splenectomy in adult patients. To clarify this relationship, prospective studies are suggested.