Significant variability in cytokine and chemokine expression after Toll-like receptor (TLR) stimulation has been observed between individuals. In this study, we determined the immunophenotypic variation in a cohort of 152 neonates associated with specific single-nucleotide polymorphisms (SNPs). We identified 23 SNPs in 12 genes of the innate immune system to be significantly associated with differential cytokine and chemokine production. SNPs in three gene families, namely STAT, IRF and SYK, accounted for most associations. These gene families are important signaling components of the innate anti-viral response. A potentially damaging non-synonymous SNP in the TLR3 gene (rs3775291) associated with significant differences in expression of interferon-γ after stimulation with the synthetic TLR3 ligand, poly (I:C). Additionally, a general increase in cytokine production was observed in subjects of Asian descent. This observation could be associated with differences in SNP genotype distribution between racial groups in our cohort. Taken together, our data suggest that particular aspects of the newborn innate response to TLR stimulation are closely associated with genetic variation. These findings provide the basis for detailed molecular dissection of cause-effect relationships between genotype and immune responses, and may account for inter-individual differences in response to vaccination and risk for infection and autoimmune disease.