The human alpha 2-macroglobulin gene was isolated in five overlapping clones. The gene spans approx. 48 kb and consists of 36 exons, from 21 to 229 bp in size and with consensus splice sites. Intron sizes range from 145 bp to 7.5 kb. The alpha 2M gene is a single copy gene in the human genome. A sequence polymorphism within the bait domain, coding for an Arg to His substitution within the primary cleavage site for trypsin, was identified in 1 of 132 individuals tested so far. Three transcription initiation sites have been identified in liver by primer extension and RNase protection assays. The most proximal, major site (+1) is preceded by a TATA-like structure (ATAAA) at -26 bp. Only 2 mRNA species were found in uterus and in cultured lung fibroblasts, while alpha 2M is not expressed to a detectable level in skin fibroblasts. The far distal transcription initiation site which is preceded by an intact TATA box and a potential HP-1 binding site is thus specific for liver.