A cloned cDNA for alpha-1-antitrypsin (alpha-1-AT) was selected from a human liver cDNA library. The identity of the clone was established by hybrid-selected translation and partial DNA sequencing. The cDNA was used as a probe to search for restriction site polymorphisms (RSPs) near the alpha-1-AT gene. Only two RSPs were found using 29 different restriction enzymes. Each of these polymorphisms resulted from the loss of a restriction site, one for EcoRI and the other for Taq I. The frequency of polymorphic restriction was calculated to be 1.1% to 2.6% of all sites tested, a figure lower than the 9.3% value observed for 12 RSPs in the human beta-globin gene cluster. Since the corresponding figure for detectable polymorphisms at the alpha-1-AT locus at the protein level is 12%, restriction enzymes are comparatively inefficient in detecting genetic variability. The basis of this inefficiency was studied by computing the nucleotide diversity from the RSP data. On the average, one in 500 to 1000 bases is polymorphic around the alpha-1-At locus. This value is comparable to that which we have calculated for the human beta-globin gene cluster and the human growth hormone gene cluster (both one in 500). These data demonstrate the limited usefulness of linked RSPs for genetic linkage studies at the alpha-1-AT locus.