Objective: The aim of this study was to determine frequency of secondary modifiers in non-transfusion dependent thalassemia. Methods: This descriptive cross sectional study was done at Fauji Foundation Hospital Islamabad. Seventy diagnosed patients of thalassemia intermedia were included. Deoxyribonucleic acid (DNA) was extracted using Chelex method. The Xmn-1 and BCL11A polymorphisms were analyzed by Amplification Refractory Mutation System (ARMS) and Restriction Fragment Length Polymorphism (RFLP) PCR. The PCR amplified products were run on Polyacrylamide Gel Electrophoresis (PAGE).Results: The Xmn-l polymorphism was seen in 26/70 (37.1%) and BCL11A polymorphism was seem in 50/70 (71.4%) of the patients. Conclusion: BCL11A and Xmn-l polymorphisms are important secondary modifiers in patients with thalassaemia intermedia in Northern Punjab.