The human adult alpha globin genes, alpha 2 and alpha 1, are contained within two tandemly arranged duplication units. Each unit spans 4 kb of DNA, and contains three homology blocks (X, Y, Z) separated by non-homologous sequences. Segmental DNA recombination processes between the two units have resulted in high frequencies of two types of deletions in certain human populations, each deletion removing one alpha globin gene from chromosome 16, (alpha-thalassemia 2). In order to study the molecular mechanisms of alpha-thalassemia 2, and of homologous DNA recombination in general in mammalian cells, we have reconstructed these two alpha-thalassemia 2 genotypes in monkey cells. The two duplication units have been cloned in an SV40 origin-containing vector, and transfected into COS 7 cells. Newly replicated plasmid DNA was isolated and analyzed by Southern blot hybridization. Homologous DNA recombination occurs with high frequencies (10-20% per kb of homology), and this generates both types of alpha-thalassemia 2 deletions on the episomes in the monkey cells. Removal of the 5' end of either one, or both, of the X blocks prior to DNA transfection affects the relative frequencies of the two alpha-thalassemia 2 genotypes in a novel way. We consider and discuss these results in terms of several alternative models. Our data suggest the existence of hot spot(s) for initiation of homologous DNA recombination, or recombination promoting element(s), in a specific region of the human adult alpha globin locus. A DNA sequence that defines the boundaries of the two duplication units, and has been implicated in the initiation of gene conversion of the two X blocks, is contained within this region.