The human 5-lipoxygenase activating protein (FLAP) gene is one of the key genes involved in the production of the cysteinyl-leukotrienes. We studied novel polymorphism of the FLAP promoter gene and attempted to clarify the relationship between this polymorphism and asthma. We sequenced the FLAP promoter region, containing the -170 to +46-bp sequence from the translational start codon, and found two homozygotes of novel alleles in the polyadenyl region which showed 21 A repeats and 18 A repeats, respectively. The frequency of the 21 A repeats was 52/71 (73.2%) in asthmatics and 39/71 (54.9%) in control subjects. The difference between these frequencies was statistically significant (P = 0.035). This is the first report of FLAP promoter gene polymorphism associated with asthma. Our data suggest that FLAP promoter gene polymorphism might play a crucial role in the pathogenesis of asthma.