Both alpha-and beta-thalassaemia syndromes are public health problems in the multi-ethnic population of Malaysia. To molecularly characterise the alpha-and beta-thalassaemia deletions and mutations among Malays from Penang, Gap-PCR and multiplexed amplification refractory mutation systems were used to study 13 alpha-thalassaemia determinants and 20 beta-thalassaemia mutations in 28 and 40 unrelated Malays, respectively. Four a-thalassaemia deletions and mutations were demonstrated. --(SEA) deletion and alpha(CS)alpha accounted for more than 70% of the alpha-thalassaemia alleles. Out of the 20 beta-thalassaemia alleles studied, nine different beta-thalassaemia mutations were identified of which beta(E) accounted for more than 40%. We concluded that the highest prevalence of (alpha-and beta-thalassaemia alleles in the Malays from Penang are --(SEA) deletion and beta(E) mutation, respectively.