Objectives: Alpha thalassaemia is wide spread in Malaysia and is a public health problem. This study aimed to describe the carrier frequencies of α‒thalassaemia and its distribution among major ethnic groups in three states of Malaysia. Methods: Educational forums were organised and study was explained to students from three schools. Students were invited to take part in the screening with parent consent. A total of 8420 adolescent students aged 16 years volunteered to participate in the study. Peripheral blood samples were analysed for complete blood counts, haemoglobin quantification and typing, and serum ferritin levels. Genomic DNA was used for screening alpha thalassaemia alleles by PCR based molecular methods. Results: We identified seven α‒globin gene defects in 341 (4.08%) students: amongst them α+‒ and α0‒thalassaemias were detected in 232 (2.77%) and 107 (1.28%) students respectively. Genotype ‒α3.7/αα was the most prevalent among sub-populations of Malay, indigenous communities of Sahab and Indian, while ‒‒SEA/αα deletion is more prevalent in Malaysian Chinese. It is estimated that 63 pregnancies annually are at risk of Hb Bart’s hydrops fetalis. Conclusions: We have demonstrated the prevalence and mutation patterns of α‒thalassaemia in the 16 year olds in three states of Malaysia. High α0‒thalassaemia deletions amongst the study subjects place these carriers at an increased risk of conceiving fetuses with HbH disease and Hb Bart’s hydrops fetalis should they choose another heterozygous partner. It is therefore highly recommended to institute community screening programmes and provide prospective carriers with genetic counselling to help them make informed choices.