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Simple Summary: Human microbiome research is rapidly expanding, including a variety of clinical medicine and public health disciplines. Commensal microbiome has a significant impact on shaping homeostasis of the organism, as well as the development of pathological states. A number of studies indicate that changes in the human microbiome could determine an oncogenic effect by, among other things, inducing chronic inflammatory response, instigating cellular antiapoptotic signals or modulation of anticancer immunity. The presence of pathogenic species also contributes to the exacerbation of the complications of the treatment applied, such as radiation-induced oral mucositis, which is the most common side effect of the treatment. A better understanding of the interplay between oral microbiome and head and neck cancers might provide an important step towards a more effective treatment for this highly malignant tumor. The following review is a complex revision of the up-to-date research on the oral microbiome and its impact on the development of head and neck cancer and radiation-induced oral mucositis. Head and neck carcinoma is one of the most common human malignancy types and it ranks as the sixth most common cancer worldwide. Nowadays, a great potential of microbiome research is observed in oncology—investigating the effect of oral microbiome in oncogenesis, occurrence of treatment side effects and response to anticancer therapies. The microbiome is a unique collection of microorganisms and their genetic material, interactions and products residing within the mucous membranes. The aim of this paper is to summarize current research on the oral microbiome and its impact on the development of head and neck cancer and radiation-induced oral mucositis. Human microbiome might determine an oncogenic effect by, among other things, inducing chronic inflammatory response, instigating cellular antiapoptotic signals, modulation of anticancer immunity or influencing xenobiotic metabolism. Influence of oral microbiome on radiation-induced oral mucositis is expressed by the production of additional inflammatory cytokines and facilitates progression and aggravation of mucositis. Exacerbated acute radiation reaction and bacterial superinfections lead to the deterioration of the patient's condition and worsening of the quality of life. Simultaneously, positive effects of probiotics on the course of radiation-induced oral mucositis have been observed. Understanding the impact on the emerging acute radiation reaction on the composition of the microflora can be helpful in developing a multifactorial model to forecast the course of radiation-induced oral mucositis. Investigating these processes will allow us to create optimized and personalized preventive measures and treatment aimed at their formation mechanism. Further studies are needed to better establish the structure of the oral microbiome as well as the dynamics of its changes before and after therapy. It will help to expand the understanding of the biological function of commensal and pathogenic oral microbiota in HNC carcinogenesis and the development of radiation-induced oral mucositis. [ABSTRACT FROM AUTHOR]