Innate and adaptive immune responses evolve as protective mechanisms against infectious microorganisms in humans. CD14 and toll-like receptors (TLRs) are examples of pattern recognition receptors that detect antigenic molecules on the surface of gram-positive (peptidoglycans, lipoteichoic acid) and gram-negative (lipopolysaccharide) bacteria. In vitro studies suggest that lipopolysaccharide is a potent inducer of interleukin-12 production that is mediated by both CD14 and TLR4. The associated increase in interferon-gamma steers our immune system away form the allergy-driven type-2 helper T cell phenotype. Epidemiological studies that shed light on the possible protective influences of natural microbial exposure on asthma and atopy development will be discussed. Recent insights into the complex mechanisms of human innate immunity suggest that genetic variability in genes encoding its components may alter the susceptibility to develop atopic disorders and other complex human diseases. The findings of these genetic association studies will be presented. Although highly conserved across a wide range of species, innate immunity genes demonstrate considerable inter-ethnic variability predominantly in the form of single nucleotide polymorphisms. The frequencies of these polymorphisms in CD14 and TLR genes in different ethnic groups will be discussed. Genetic variation in these genes may also play a role in the development of other human diseases that have an inflammatory component. Lastly, the prospect of using immunomodulatory agents targeting on the innate immunity to treat or even prevent asthma and other allergic diseases will be discussed.