Karyotypic homology in relation to human chromosome 9 (HSA 9) was studied through comparative mapping of the immunoglobulin-processed pseudogene C epsilon 3 (IGHEP2) in primates. IGHEP2, which has been mapped to 9p24.2 --> p24.1 in the human genome, was assigned to PTR 11q34 (common chimpanzee), PPA 11q34 (pygmy chimpanzee), PPY 13q16 (orangutan), HLA 8qter (white-handed gibbon), HAG 8qter (agile gibbon), and MFU 14q22 (Japanese macaque) by fluorescence in situ hybridization. To verify the breakpoints of presumed pericentric inversions on the ancestral great ape chromosomes, three DNA markers on HSA 9, cCI9-37 (9q22.1 --> q22.2), cCI9-135 (9q22.32 --> q22.33), and cCI9-208 (9p13.3 --> p13.2), were also assigned to PTR/PPA 11p11 (cCI9-37 and 135), PTR/PPA 11q22 (cCI9-208), PPY 13q22 (cCI9-37 and 135), and PPY 13q12 (cCI9-208). These data more clearly define the position of the breakpoints of pericentric inversions that occurred in the human-chimp ancestral and chimpanzee ancestral chromosomes and support the hypothesis of HSA 9 genesis previously derived from banding analyses of HSA 9 and its homologs.