We studied the organization and origin of three orphon regions, VH-F, D5-a, and D5-b, of the human immunoglobulin heavy-chain gene using yeast artificial chromosomes. VH-F and two D5 regions were mapped to chromosome bands 16p11 and 15q11-q12, respectively, by using human/rodent somatic cell hybrids and fluorescence in situ hybridization. No D5 segments were found on chromosome 14, in contradiction to previous reports. The VH-F region consists of 7 VH segments and encompasses 160 kb of DNA. A cluster of VH segments homologous to the VH-F region orphons was found in the region 245-430 kb (V2-26 to V3-11) upstream of the JH cluster on chromosome 14. Comparison of VH sequences between the VH-F and the chromosome 14 loci indicates that the translocation of the VH-F region took place, at the earliest, 20 x 10(6) years ago. The D5-a and D5-b regions were obtained in two independent contigs. The former contains only D segments in 140 kb of DNA, while the latter carries 3 VH segments downstream of D segments in 110 kb of DNA. V54, one of these VH orphon segments, is about 95% homologous to V1-18, which is located within the putative ancestor of the VH-F region on chromosome 14. Furthermore, the region detected by two DNA probes flanking the V54 segment was found only in the proximity of V1-18 within the 0.8-Mb VH region on chromosome 14. These results suggest that the two orphon loci on chromosomes 15 and 16 may have been translocated simultaneously.