In one program of newborn screening to detect deletional alpha-thalassemia with microarray, the microarray result of a 10-month-old girl showed that she was positive for the rightward deletion junction fragment, the Southeast Asian deletion junction fragment and alpha2.The girl and her parents were subjected to haematological and molecular analysis.The haematological data revealed that the family presented a typical alpha-thalassemic trait. The molecular analysis showed that the girl and her mother were compound heterozygosity for HKalpha alpha allele and Southeast Asian deletion allele, and her father is compound heterozygosity for alpha alpha allele and Southeast Asian deletion allele.We have detected a hitherto unreported compound heterozygosity for HKalpha alpha allele and Southeast Asian deletion allele. This case will provide some clinical implications for PCR-based diagnosis for deletional alpha-thalassemia.