IgE-dependent activation of mast cells and basophils through the high-affinity IgE receptor (Fc(epsilon)R1) is involved in the pathogenesis of allergen-induced immune responsiveness in atopic disease including bronchial asthma. We genotyped 650 children for allelic determinants at two polymorphic sites, -109T/C and E237G, in the Fc(epsilon)R1beta gene by SNP-IT assays using the SNP stream 25K system. Distributions of the genotype and allele frequencies of Fc(epsilon)R1beta -109T/C and E237G polymorphisms were significantly associated with atopy (P < 0.05) and elevated serum IgE levels. However, differences in the E237G polymorphism did not reach statistical significance after adjustment for multiple comparisons. The genotypes TC or CC at -109T/C were associated with decreased forced expiratory flow(25-75%) in children with asthma (P < 0.05), but this did not reach statistical significance after correction for multiple comparisons. In addition, haplotype 1 (T-A) was associated with atopy susceptibility (P = 0.0069). Analysis of genotype distributions of haplotypes demonstrated a significantly lower PC(20) for homozygous -/- diploids compared with homozygous Ht1/Ht1 (P = 0.0261). Polymorphisms in the Fc(epsilon)R1beta gene confer susceptibility to atopy in Korean children and may have a disease-modifying effect on airways of asthmatic patients.