Objective: The thalassemias are the most common monogenic disorders with a genetically determined reduction in the rate of one or more types of normal haemoglobin polypeptide chain resulting in a decrease in the amount of haemoglobin involving the affected chain. Beta thalassemia is a highly heterogeneous disorder in its phenotype, geographical distribution and molecular mechanism. The main objective was to study the different mutation in the nepalese population. Methods: DNA was extracted from the 26 clinically diagnosed blood sample and Amplification Refractory Mutation System - Polymerase Chain Reaction (ARMS PCR) was used for amplification to analyze mutations in hbb gene and 2% gel electrophoresis was used for visualization of PCR products Results: Among 26 β-thalassemia major patients, 13 (50%) had IVS 1-5 (G>C) mutation, 8 (30.76%) had 6l9bp deletion, 2 (7.69%) CD 8/9 (+G), 1 (3.84%) CD 15 (G>A), 1 (3.84%) had -88 (C>T) mutation whereas CD41/42 (-TCTT) was not detected in any of the patients. Among the patients with 619 bp deletions 2 (25%) were homozygotes and 6 (75%) were heterozygotes Conclusion: This is the baseline study to assist in the regulation of proper new health policies which will impact in the proper diagnosis and treatment.