A new large deletion from the human alpha-globin gene cluster is characterized. It involves at least 39 kb and includes the two alpha-globin genes, the theta 1-gene, all the pseudogenes, and the two hypervariable regions (HVRs), interzeta-HVR and alpha-globin 3'HVR. The conserved zeta-globin gene has been identified in various restriction fragments of abnormal size. The new deletion was found in four unrelated Israeli patients with Hb H disease, all originating in Yemen, and has been designated--YEM. It is the only two-gene deletion identified in this ethnic group.