The toll-like receptor 4 (TLR4) plays a key role in the activation of innate immune response participating in the recognition of lipopolysaccharides. Changes in the innate immune response are involved in the pathogenesis of some metabolic disorders such as metabolic syndrome and type 2 diabetes mellitus (Met-S and T2DM). It has been recently shown the role of gut microbiota in the perpetuation of both insulin resistance and low-grade chronic inflammation. Some studies have reported that TLR4 D299G polymorphism is associated with metabolic disorders, however results have been inconsistent. Two recent meta-analyses showed that D299G is associated with inflammatory bowel disease and gastrointestinal cancers risk, two pathological states in which the luminal microbial flora-host cells interaction may be implicated. We conducted a systemic review of the published data considering all eligible published studies (six studies with 1696 cases and 3388 controls for D299G) and a meta-analysis was performed to evaluate the association between TLR4 D299G polymorphism and the risk for metabolic disorders. Five studies were identified for T2DM: three corresponding to Caucasian populations and two to mixed populations. The remaining study analyzed Met-S in a Caucasian population. We observed a significant association between D299G polymorphism and metabolic disorders (T2DM and Met-S) risk (OR = 0.566, 95 % CI: 0.347–0.925, p = 0.023) particularly in Caucasians. No association was found in mixed population subgroup. Our meta-analysis identified that the AG/GG genotypes of D299G are associated with decreased metabolic disorders risk.