The structural organization of the gene for the E3 subunit of the human alpha-ketoacid dehydrogenase complexes, dihydrolipoamide dehydrogenase (DLD), and its upstream elements have been determined by restriction endonuclease mapping and DNA sequence analysis of overlapping genomic clones. The gene is approximately 20 kb long. It contains 14 exons ranging in size from 69 to 780 bp and 13 introns ranging in size from 93 bp to 7.0 kb. All splice donor and acceptor sites conform to the GT/AG rule. The 5' ends of mRNA transcripts upstream from the translation initiation codon were determined by primer extension assay. A "CAAT box"-like sequence is present at 39 bp upstream of the presumptive cap site and the 5' flanking region has been sequenced up to 2.0 kb upstream. There are several sequences compatible with presumptive promoter elements, including an Sp1 binding site, a nuclear respiratory factor 1 site, two cyclic AMP response element binding sites, and a possible negative response element present in the insulin promoter. A 313-bp segment from -2076 to -1763 is 89% homologous to a recently described pTR5 repetitive element found in the human genome.