It is likely that multiple genes contribute to immunoglobulin (Ig)E production. Co-stimulatory molecules are crucial for the cross-talk between antigen presenting cells and T-lymphocytes which drives the IgE response.We evaluated gene–gene interactions of haplotype tagging polymorphisms in a pathway of 24 co-stimulatory genes in relation to serum IgE levels. We assessed this at ages 1–2 yrs and 6–8 yrs in 3,062 Dutch children from a pooled data set of three birth cohorts: PIAMA (Prevention and Incidence Asthma and Mite Allergy), PREVASC (Prevention of Asthma in Children) and KOALA (Child, parents and health: lifestyle and genetic constitution).Single- and multi-locus associations with serum IgE levels (3rdversus1st tertile) were evaluated by Chi-squared tests and the multifactor dimensionality reduction (MDR) method in the following co-stimulatory genes:VTCN1,TNFRSF4,TNFRSF18,TNFRSF14,TNFSF18,TNFSF4,CD28,CTLA4,ICOS,PDCD1,BTLA,CD80,CD86,HLA-G,CD274,PDCD1LG2,CD276,LILRA4,LILRB1,LILRB2,LILRB4,CD40,ICOSLG, andCD40LG. We found multiple statistically significant single-locus(S)and multi-locus(M)associations for the genesVTCN1SM,TNFSF18SM,TNFSF4S,CD28S,CTLA4M,ICOSS,BTLAM,CD80M,CD86SM,CD274SM,PDCD1LG2M,LILRA4SM,LILRB4M, andCD40SMwith serum IgE. Two-locus interactions ofCD86withVTCN1andCD274withLILRA4were confirmed by logistic regression.In conclusion, serum IgE levels are regulated by multiple gene–gene interaction effects in the co-stimulatory pathway. We suggest using research strategies that model multiple gene–gene interactions in genetic studies.