Alimentary mucositis is a major clinical problem. Patients with mucositis are at significantly increased risk of infection and are often hospitalized for prolonged periods. More importantly, these patients often have to undergo reductions in their cytotoxic therapy, which may lead to reduced survival. Unfortunately, there are very limited therapeutic options for mucositis and no effective prevention. The human gut microbiome is receiving increased attention as a key player in the pathogenesis of alimentary mucositis with recent literature suggesting that changes in bacteria lead to mucositis. The bacteria which are found throughout the gut are tightly regulated by the toll-like receptor (TLR) family which currently has 13 known members. TLRs play a critical role in gut homeostasis and bacterial regulation. Furthermore, TLRs play a critical role in the regulation of nuclear factor kappa B, a key regulator of alimentary mucositis. However to date, no research has clearly identified a link between TLRs and alimentary mucositis. This critical literature review seeks to correct this.