BACKGROUND AND OBJECTIVES: Both biomechanical and emotional factors may contribute to the development of work-related musculoskeletal disorders in physical therapists working at a hospital, but we still do not know if these professionals present musculoskeletal symptoms related to the sector and working time. The objective of this study was to compare the self-report of pain and musculoskeletal discomfort of the physical therapists working in the intensive care unit and ward of a university hospital and retrospectively evaluate, 12 months of work, self-report of pain and musculoskeletal discomfort of physiotherapists in these sectors. METHODS: The self-report of pain and the musculoskeletal discomfort of the 18 physical therapists working in this hospital were evaluated by the Nordic Musculoskeletal Questionnaire in the admission period (T0) and after 12 months (T1). RESULTS: No association was found between the self-report of pain and musculoskeletal discomfort and the working sector of these professionals. However, there was a temporal association between the self-report of pain and musculoskeletal complaints in the intensive care unit sector in the following regions: neck (p=0.043), shoulders (p=0.009), upper back (p=0.043), lower back (p=0.043) and hip and thigh region (p=0.027). The second shift of these professionals was not associated with pain and musculoskeletal discomfort. CONCLUSION: The self-report of pain and musculoskeletal discomfort of physical therapists of this university hospital, both in the admission period (T0) and after 12 months of work (T1) was not associated with the sector in which they work. However, after 12 months, the physical therapists working in the intensive care unit showed an increase in the amount of self-report of pain and musculoskeletal discomfort. Pain and musculoskeletal discomfort in physiotherapists of the intensive care unit and ward of a university hospital: a retrospective cohort study Dor e desconforto musculoesquelético em fisioterapeutas da unidade de terapia intensiva e enfermaria de um hospital universitário: um estudo de coorte retrospectivo