Infectious diseases exert a constant evolutionary pressure on the innate immunity genes. TLR4, an important member of the Toll-like receptors family, specifically recognizes conserved structures of various infectious pathogens. Two functional TLR4 polymorphisms, Asp299Gly and Thr399Ile, modulate innate host defense against infections, and their prevalence between various populations has been proposed to be influenced by local infectious pressures. If this assumption is true, strong local infectious pressures would lead to a homogeneous pattern of these ancient TLR4 polymorphisms in geographically close populations, while a weak selection or genetic drift may result in a diverse pattern. We evaluated TLR4 polymorphisms in 15 ethnic groups of Iran, to assess whether infections exerted selective pressures on different haplotypes containing these variants. The Iranian subpopulations displayed a heterogeneous pattern of TLR4 polymorphisms, comprising various percentages of Asp299Gly and Thr399Ile alone or in combination. The Iranian sample as a whole showed an intermediate mixed pattern when compared with commonly found patterns in Africa, Europe, Eastern Asia and Americas. These findings suggest a weak or absent selection pressure on TLR4 polymorphisms in the Middle-East, that does not support the assumption of an important role of these polymorphisms in the host defence against local pathogens.