Thermolabile (TL) phenol sulfotransferase (PST) catalyzes the sulfate conjugation of phenolic monoamines such as dopamine. The level of activity of TL PST in at least one human tissue, the blood platelet, is controlled by a genetic polymorphism. We previously cloned and expressed a cDNA for human liver TL PST and localized its gene, STM, to human chromosome 16p11.2, a region of the chromosome to which the Batten disease gene is also localized. A cDNA for human brain TL PST with an identical open reading frame (ORF) has also been cloned. We have now isolated the human TL PST gene, STM, and have characterized its structural organization as an additional step toward understanding molecular mechanisms involved in the regulation of levels of TL PST activity in human tissue. STM consists of ten exons and nine introns, with a total length of approximately 8.4 kb. Exons range from 88-499 bp in length, while introns vary from 89-1855 bp. Many of the exon-intron splice junctions in STM are located at positions identical to those of splice junctions in the human dehydroepiandrosterone (DHEA) ST gene, STD, and the rat phenol or aryl ST gene. The first two STM exons are represented in the 5'-UTR of a longer TL PST cDNA expressed in both brain and liver, while exon III is represented in a shorter cDNA 5'-UTR expressed in both tissues. These observations suggest alternative transcription initiation and/or alternative splicing as explanations for the existence of TL PST mRNA species with two different 5'-UTRs. 5'-Flanking region(s) of STM contained neither canonical TATA nor CCAAT elements, but they did contain pyrimidine-rich stretches. Northern blot analyses showed that an mRNA species approximately 1.4 kb in length was expressed in human liver, kidney, lung, small intestine, spleen and leukocyte. Molecular cloning and structural characterization of STM will make it possible to study molecular genetic mechanisms involved in the regulation of TL PST activity in human tissue.