We here report the molecular characterization of an Indonesian ovalocytosis. The analysis of genomic gene by polymerase chain reaction shows that the individual has two amplified products from a region encompassing exon 11 of the erythrocyte band 3 gene. The sequence of the larger product matched completely with that of normal individuals. In the sequence of the smaller product, 27 nucleotides within exon 11 disappeared. The deletion removes a total of nine amino acids in the boundary of cytoplasmic and membrane domains of band 3 protein, a membrane anion transporter protein. This is the first report to confirm the heterogeneous presence of an altered membrane band 3 protein in Indonesian ovalocytosis.