Pericentric inversion of chromosome 9 is a common chromosomal aberration that may be involved in the pathogenesis of several types of cancer. Screening for structural balanced chromosomal aberrations in 58 patients with ovarian carcinoma found a patient with inv(9)(p11;q13) who had repeated spontaneous abortions. To define the breakpoint at the 9p11 region, the human 9p11-specific CEPH-YAC library was first screened with fluorescence in situ hybridization (FISH) analysis, resulting in isolation of the YAC clones 961d9 and 954b9 spanning the breakpoint. Next, screening with FISH analysis of the cosmid library constructed from 961D9 isolated 3 cosmid clones that included the breakpoint. DNA sequence analysis showed that the cosmid clones spanned the 57.7-kb sequence, which contained the FGF7 [keratinocyte growth factor (KGF)]-like gene including exons 2 and 3. FISH analysis showed that the 57.7-kb sequence was duplicated from the 9p11 region to the 9q13 region on the aberrant chromosome 9. Southern blot analysis showed multiple FGF7-like genes in the 9p11 region which were also duplicated to the 9q13 region on the aberrant chromosome 9. Because the FGF7-like genes are located at 9p11 and 9q13, our results are consistent with the hypothesis that the FGF7-like genes at 9p11 and 9p13 initiate the pericentric inversion of chromosome 9. Analysis of surgical specimens of ovarian cancer with the reverse transcription-polymerase chain reaction and immunohistochemical staining showed overexpression of the FGF7 gene in 4 of 9 stage I or II cases and in 10 of 11 stage III or IV cases. These findings suggest that FGF7 plays a significant role in the development of ovarian cancer.