The structure and sequence of the human red blood cell anion exchanger (EPB3, AE1, band 3) gene was determined by analysis of genomic and cDNA clones. The gene extends over 18 kb and consists of 20 exons. The cDNA sequence comprises 4,906 nucleotides [excluding the poly(A) tail]. There is extensive similarity between the human and mouse AE1 gene, although the latter covers 17 kb. The additional sequence present within the human AE1 gene compared with the mouse gene is mainly caused by the presence of 6 Alu repetitive units in the human gene between intron 13 and exon 20, one of which is within the 3′ noncoding region of the cDNA. Two potential promoter regions within the human AE1 gene are located so that they could give rise to the different transcripts found in erythroid cells and in the kidney. The kidney transcript would lack exons 1 through 3 of the erythroid transcript. The translation initiator downstream to the human kidney promoter would give rise to a protein with a 20 amino acid section at the N-terminus that is not present in the erythroid human AE1 protein or the rodent kidney AE1 proteins.