Fc receptors (FcR) play an important role in immune regulation. This might be linked to the variability in immune response, therefore relating to the pathogenesis of atopic diseases. The aim of the present study was to evaluate the Fc gamma RIIIa gene polymorphism in Turkish children with asthma and allergic rhinitis. The study included 364 atopic children (184 bronchial asthma, 180 allergic rhinitis) and 234 healthy subjects as the control group, aged between 5 to 16 years. Patients were recruited from outpatient clinics of allergy and general pediatric care. Plasma IgE concentrations were measured by immunoassays and skin prick test was done in children with atopic diseases. The Fc gamma RIIIa gene polymorphism was determined using the polymerase chain reaction method. Distribution of V158V genotype was significantly different among patient groups compared to controls (for asthmatic children OR: 5.33, 95% CI: 2.80-10.23, p < 0.001; for allergic rhinitis OR: 3.25, 95% CI: 1.75-6.07, p = 0.001). Distribution of 158 V allele was significantly different among asthmatic children (OR: 2.20, 95% CI: 1.65-2.92, p < 0.001) and allergic rhinitis patients (OR: 1.77, 95% CI: 1.32-2.35, p < 0.001) compared to healthy controls. Our study shows that the V158V genotype in Fc gamma RIIIa gene polymorphism may be a genetic risk factor for the development of atopic diseases.