Seven genomic DNA clones representing the rat alpha 2-macroglobulin gene were isolated and characterized. The cloned sequence covered the entire gene (48 kilobases) plus 2 kilobases of 3'- and 13.7 kilobases of 5'-flanking sequences. A restriction cleavage map of the gene was produced, and the restriction cleavage pattern of genomic DNA suggested that the alpha 2-macroglobulin gene is a single-copy gene. A 7.7-kilobase fragment from the 5'-terminal region and a 250 base pair fragment from the 3'-terminal region of the gene were sequenced, and the 3' end of the gene was mapped. The sequenced 5'-terminal fragment contained 4.5 kilobases of 5'-flanking sequences plus the first three exons and two introns of the gene. Two transcription start sites, a minor and a major site, located 65 nucleotides apart, were defined by primer extension, S1 mapping, and RNaseH experiments. During an acute-phase response, transcription from both sites was induced in the liver, and over 90% of the transcripts originated from the major site. Very high concentrations of alpha 2-macroglobulin mRNA originating from both start sites were also found in the uterus but not in the liver of pregnant females. A glucocorticoid response element (GRE), a conserved consensus sequence for a potential glucocorticoid receptor DNA binding site, was found by computer search in the promoter-proximal 5'-flanking region of the alpha 2-macroglobulin gene.