Objective: Dysbiosis favours translocation of endotoxins into the plasma. Increased endotoxins leads to metabolic endotoxaemia, which is associated with development of inflammation in type 2 diabetes mellitus (T2DM) patients. This systematic review highlights the association between gut microbiota composition and their effects on biochemical parameters in T2DM patients. Methods: Literature search was conducted using three electronic databases with restriction to English language. Studies were selected according to inclusion criteria and data of potential studies were extracted independently by two authors. Relevant data were then assessed for risk of bias. Results: A total of 10 case-control studies, which involved T2DM patients and healthy individuals, were included in this review. An increase in the abundance of Lactobacillus species and reduction in butyrate producers (i.e. Clostridium, Roseburia and Eubacterium species) was positively correlated with HbA1c and FBG. An increase in C. clostridioforme, a butyrate producer, was also positively correlated with triglyceride level. In contrast, there was no clear association between inflammatory markers and the microbiota profile. Whilst Clostridium spp. and Eubacterium spp. were reported to decrease, a higher number of Bifidobacterium spp., Lactobacillus spp. and Enterococcus spp. were observed in patients consuming metformin and α-glucosidase inhibitors, respectively. Conclusion: Altered gut microbiota composition in T2DM patients might be important in the pathogenesis of T2DM. Changes of gut microbiota composition appear to be linked to glycaemic parameters and triglycerides level.