Interleukin-13 (IL-13) has a pivotal role in the pathway of immunoglobulin E (IgE). Cord serum IgE has been suggested to be associated with allergy later in life, yet less affected by environmental exposures. We investigated the association of the interleukin-13 gene (IL13) polymorphisms on cord serum IgE. In the Isle of Wight birth cohort (UK, 1989-1990), cord serum IgE was measured using the ULTRA EIA kit and was dichotomized at 0.5 kU/l (n = 1358). Five single nucleotide polymorphisms (SNPs: rs1800925 in promoter, rs2066960 in intron 1, rs1295686 in intron 3, rs20541 in exon 4 and rs1295685 in exon 4) in IL13 were genotyped by pyrosequencing method. Linkage analysis using Haploview software revealed that rs1295686, rs20541 and rs1295685 were in strong linkage disequilibrium. Logistic regression and Armitage-Cochran test were used and gene association analysis included 798 children. Confounders were maternal age; maternal smoking, household dog, and household cat during pregnancy; season of birth; sex; position of child in family; and birth weight. SNP rs1295685 was associated with raised cord serum IgE (p = 0.031). This is the first report that shows an association between IL13 polymorphism and cord serum IgE.