It is thought that the incidence and severity of cancer chemotherapy-associated mucositis is caused in part by changes in the oral bacterial microflora. This systematic review examined the role of oral bacterial microflora changes in the development of oral mucositis during chemotherapy. Thirteen prospective clinical trials were identified, involving 300 patients with 13 different cancer diagnoses. There was great variability in patient populations, bacterial sample collection methodology, and oral sample sites. No clear pattern regarding qualitative and quantitative oral flora changes emerged among these studies. The most frequent Gram-negative species isolated during chemotherapy were from the Enterobacteriaceae family, Pseudomonas sp. and E. coli. The most common Gram-positive species isolated were Staphylococcus sp. and Streptococcus sp. Five studies assessed the role of oral flora changes in the genesis of oral mucosal changes, with no consensus among them. More detailed studies are required to understand the relationship between chemotherapy, alterations in the nature and magnitude of the oral microflora, and the presence of mucositis.