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To provide an updated perspective on the use of probiotics as adjuvant treatment strategy for patients suffering from or at risk of developing mucositis.Studies suggest that oral and intestinal microbiota could be relevant to mucositis development and treatment, but no clear high-risk pattern has been identified and no single probiotic formulation has emerged from human clinical trials for strong recommendation. Promising results from available clinical trials suggest their use in patients with peri-implant mucositis or at risk of anticancer treatment-related oral or intestinal mucositis. In general, a positive effects of Lactobacillus species is becoming consistent, particularly Lactobacillus reuteri, in the treatment of peri-implant mucositis and Lactobacillus brevi CD2 in the prevention of chemoradiotherapy-related oral mucositis. However, several limitations still need to be addressed by future research. Nonetheless, their use appears to be safe. Therefore, decision to consider the use of probiotics ultimately depends on the preference of the clinicians.In the ongoing era of ‘precision medicine’, efforts should be directed toward the identification of high-risk patient populations which could benefit most from targeted interventions with probiotics enabling an improvement of clinical outcomes and quality of life in a cost-effective manner.