The enzyme lactase, which is responsible for the digestion of dietary lactose, is present in the intestine of some adults but not others. As a means of providing a platform to explore the molecular basis of this nutritionally relevant genetic variation we have screened for polymorphism in several regions of the lactase gene. In each case simple polymerase chain reaction-based procedures (including single-strand conformation analysis and denaturing gradient gel electrophoresis) were used, combined with silver staining as a method of detection. Allelic variation was found at 6 different sites. One previously published polymorphism was also tested. The frequencies of the alleles were determined in more than 100 unrelated individuals of the Centre d'Etude du Polymorphisme Humain (CEPH) panel, and the haplotypes were deduced. A region of linkage disequilibrium was observed, which spans the whole coding region of the lactase gene (approximately 60-70 kb); there were only 3 common haplotypes in this population. When the CEPH sample was subdivided according to the population of origin (France or Utah) the haplotype frequencies were shown to be markedly different.