Familial hypercholesterolemia (FH) is a common autosomal dominant disorder caused by a defect in the low-density-lipoprotein (LDL) receptor, distrupting the normal control of cholesterol metabolism. Fourty-two unrelated heterozygotes for FH were screened to detect structural rearrangements in the LDL receptor gene. Genomic DNA was analyzed by Southern blot hybridization to probes encompassing exons 1-18 of the LDL receptor gene to detect large structural rearrangements. A novel deletion mutation was detected in a FH pedigree. Southern blot analysis using the exon-specific probes revealed that this mutation elimianted exons 9, 10, 11, and 12. Detailed restriction mapping and sequence analysis mediated long PCR demonstrated that this mutation was 5.72kb deletion extending from intron 8 to 12, and has occurred between two Alu-repetitive sequence that are in the same orientation, one in intron 8 and the other in intron 12. We suggest that in this patient the deletion is caused by an unequal crossing-over event that occured between two homologous chromosomes at meiosis.