A DNA fragment containing the deletion junction region from a Japanese individual with homozygous delta beta-thalassemia has been cloned. A clone containing the normal DNA surrounding the 3' breakpoint of this deletion and a clone carrying the G gamma- and A gamma-globin genes of this patient were also isolated. Sequences of the deletion junction and both gamma-globin genes were determined. A comparison of these sequences with previously determined sequences of the normal counterparts revealed that the 5' breakpoint is located between 2,134 and 2,137 base pairs (bp) 3' to the polyA site of the A gamma-globin gene, the 5' breakpoint is located just downstream of the 3' border of the fetal gamma-globin duplication unit, and no molecular defects are evident within the gamma-globin gene region. A comparison between the sequences of the normal DNA surrounding the 3' breakpoint and the normal DNA surrounding the 5' breakpoint shows that deletion is the result of a nonhomologous recombination event. There are A+T-rich stretches near the 5' and 3' breakpoints in the normal DNA, and a portion of an Aly repeat is located in the region 3' to the 3' breakpoint. Southern blot analysis using probes 3' to the beta-globin gene showed that the deletion extends in the 3' direction further than any other deletions associated with delta beta-thalassemia and hereditary persistence of fetal hemoglobin (HPFH) heretofore reported. These results are discussed in terms of the mechanism generating large deletions in mammalian cells and three models for the regulation of gamma-globin and beta-globin gene expression in humans.