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Background Physiotherapy and occupational therapy are two professions at high risk of work related musculoskeletal disorders (WRMD). This investigation aimed to identify risk factors for WRMD as perceived by the health professionals working in these roles (Aim 1), as well as current and future strategies they perceive will allow them to continue to work in physically demanding clinical roles (Aim 2). Methods A two phase exploratory investigation was undertaken. The first phase included a survey administered via a web based platform with qualitative open response items. The second phase involved four focus group sessions which explored topics obtained from the survey. Thematic analysis of qualitative data from the survey and focus groups was undertaken. Results Overall 112 (34.3%) of invited health professionals completed the survey; 66 (58.9%) were physiotherapists and 46 (41.1%) were occupational therapists. Twenty-four health professionals participated in one of four focus groups. The risk factors most frequently perceived by health professionals included: work postures and movements, lifting or carrying, patient related factors and repetitive tasks. The six primary themes for strategies to allow therapists to continue to work in physically demanding clinical roles included: organisational strategies, workload or work allocation, work practices, work environment and equipment, physical condition and capacity, and education and training. Conclusions Risk factors as well as current and potential strategies for reducing WRMD amongst these health professionals working in clinically demanding roles have been identified and discussed. Further investigation regarding the relative effectiveness of these strategies is warranted.