Regulatory elements linked to the beta-globin gene cluster modulates gamma-globin gene expression. The location of all of these elements and their mechanisms of action are still incompletely defined. Phylogenetically conserved DNA within the beta-globin gene cluster locus control region (LCR), but outside the core sequences of its hypersensitive sites (HS), were identified and we searched for any differences between HS 3 and HS 2, and HS 2 and HS 1, among patients with sickle cell anemia with different levels of Hb F who were homozygous for the common haplotypes. DNA was amplified with and without GC clamps, digested with restriction endonucleases, and examined by denaturing gradient gel electrophoresis (DGGE). We found limited fragment size diversity. However, the type of differences found and their distribution among haplotypes did not suggest that they represented distinctive changes that might explain the differential expression of the gamma-globin genes in sickle cell anemia.