IVS-1 25bp deletion in the β-globin gene is rare entity in South East Asia region. We report the first case of β-thalassaemia major in a Malay girl from Malaysia with IVS-1 25bp deletion heterozygously compounded with IVS 1-5 (G>C) consensus mutation. Clinical presentation and molecular diagnostic procedures was described. Molecular diagnosis of rare and emerging thalassaemia alleles can be challenging. Sequence haplotype analysis using classical SNP markers for the family members suggest the IVS-1 25bp deletion probably was derived from Middle East.