We assessed the prevalence of “probable” asthma, allergic rhinitis, atopic dermatitis, and positive skin test (atopy) among genotype groups of GM-CSF 545G/A, 3606T/C, and 3928 C/T polymorphisms in a cohort of 370 children at high risk for atopy and atopic diseases. The homozygous GM-CSF 545AA genotype was associated with asthma at 12 months (relative risk [RR] = 3.4, p = 0.021). The GM-CSF genotypes containing 3606T were associated with dermatitis at 12 months (RR = 2.5, p = 0.037) and 24 months (RR = 2.5, p = 0.009). The homozygous GM-CSF 3606 TT genotype was associated with atopy at 12 months (RR = 3.89, p = 0.002). The homozygous GM-CSF 3928 CC was associated with dermatitis at 12 months (RR = 6.1, p = 0.0002); the GM-CSF genotypes containing 3928C were associated with dermatitis at 24 months (RR = 2.0, p = 0.049). Our data suggest that GM-CSF 545A, 3606T, and 3928C alleles are risk factors for the development of atopy and atopic diseases.