Mitochondrial FAD-linked glycerol-3-phosphate dehydrogenase (mtGPDH) is one of the two enzymes of the glycerol phosphate shuttle. This shuttle transfers reducing equivalents from the cytoplasm to the mitochondria in a unidirectional, exothermic manner. Here, the isolation and characterization of the rat nuclear gene (Gpd2) encoding mtGPDH is reported. The mtGPDH gene spans 100 kb and consists of 17 exons. The use of alternate promoters was suggested by the presence of three different first exons and confirmed by transient expression for two of them. The first exons are expressed in a tissue-restricted manner. Exon 1a was found primarily in brain, exon 1b was used in all tissues examined, and exon 1c was detected predominantly in testis. Depending on the tissue, different transcript lengths were also observed: 5.9 kb (all tissues), 3.6 kb (skeletal muscle), and 2.5 kb (testis). The length isoforms are attributable to alternate splicing and polyadenylation site use. Very high mtGPDH mRNA levels were found in brown adipose tissue, 75 fold greater than in white adipose tissue. Thyroid hormone increased mtGPDH mRNA levels in liver and heart but not in brown adipose tissue, brain, or testis. This pattern corresponds to that of thyroid hormone-induced oxygen consumption and is consistent with a role for mtGPDH in thyroid hormone-induced thermogenesis. Both thyroid-responsive and nonresponsive tissues used promoter lb, suggesting that tissue-specific factor(s) contribute to the tissue-restricted responsiveness to thyroid hormone.