Mucositis is a challenging treatment-related complication in children receiving therapy for cancer. The conduct of clinical trials that investigate mucositis prevention and treatment requires adequate evaluation of the oral cavity. However, few instruments to measure mucositis in children have been appropriately developed or evaluated. A focus group of nine health care professionals with expertise in mucositis assessment, oral assessment in children and paediatric cancer aimed to determine the challenges and possible solutions to mucositis assessment in children. The results led to the identification of several areas of concern that included: (1) challenges in oral assessment in children related to age and cooperation, (2) the need for proxy responses while recognizing the challenges of reporting pain and function attributed to oral mucositis, (3) the need for an instrument that is simple, quick to complete, and easy to use in almost all children and (4) educational considerations. The results provide a basis from which guidelines for the oral assessment of mucositis in children can begin. This information could be used to aid in the development of a new scale for the assessment of oral mucositis in children.