Toll-like receptor (TLR)-mediated innate immune responses are important in early host defense. Using a candidate gene approach, we previously identified genetic variation within TLR1 that is associated with hyper-responsiveness to a TLR1/2 agonist in vitro and with death and organ dysfunction in patients with sepsis. Here we report a genome-wide association study (GWAS) designed to identify genetic loci controlling whole blood cytokine responses to the TLR1/2 lipopeptide agonist, Pam(3)CSK(4) (N-palmitoyl-S-dipalmitoylglyceryl Cys-Ser-(Lys)(4)) ex vivo. We identified a very strong association (P<1 × 10(-27)) between genetic variation within the TLR10/1/6 locus on chromosome 4, and Pam(3)CSK(4)-induced cytokine responses. This was the predominant association explaining over 35% of the population variance for this phenotype. Notably, strong associations were observed within TLR10, suggesting that genetic variation in TLR10 may influence bacterial lipoprotein-induced responses. These findings establish the TLR10/1/6 locus as the dominant common genetic factor controlling interindividual variability in Pam(3)CSK(4)-induced whole blood responses in the healthy population.