The pyruvate dehydrogenase (PDH) complex converts pyruvate to acetyl CoA, an essential step in aerobic glucose metabolism. We have previously shown that the gene for the E1 alpha subunit of this complex, expressed in somatic tissues, is located on band p22.1 of the human X chromosome. This gene, PDHA1, contains 10 introns and spans approximately 17 kb. An autosomal locus, PDHA2, showing significant cross-hybridization with a PDH E1 alpha cDNA probe, was detected on chromosome 4, in the region q22-q23. We here report the isolation of human testis-specific PDH E1 alpha cDNA clones. The similarity with the X chromosome-linked cDNA coding sequence at the nucleotide level is 84%. Specific amplification using the polymerase chain reaction confirmed the presence of a testis-specific mRNA and indicated that postmeiotic spermatogenic cells express this subunit. In situ hybridization with a unique probe from the 3' untranslated region of the testis-specific cDNA showed that the gene for this form of PDH E1 alpha is localized on chromosome 4 in the region q22-q23. The autosomal human gene was isolated from a chromosome 4-specific genomic library. The transcribed region of this gene is identical to the testis-specific cDNA sequence. It completely lacks introns and possesses characteristics of a functional processed gene.