Abstract Background Musculoskeletal disorders are common in the general population and a leading cause for care seeking. Despite the large number of patients with musculoskeletal disorders seeking care, little is known of the clinical course, pathways and predictors of healthcare utilization among these patients. The purposes of the study were to 1) describe the clinical course and related healthcare utilization in primary care physiotherapy and secondary healthcare among patients with neck, shoulder and low-back pain treated in physiotherapy practice, and 2) identify independent clinical, socio-demographic, psychological and general health predictors of healthcare utilization. Methods The study was a prospective cohort study of patients seeking physiotherapy treatment for neck, shoulder, or low-back pain in physiotherapy practices across Denmark. A total of 759 physiotherapy patients completed questionnaires containing information on clinical course and potential predictors of healthcare utilization. Healthcare utilization was obtained from the Danish National Health Service Register and National Patient Register. Associations between potential predictors and low/high primary care physiotherapy utilization and hospital contacts in relation to specific neck, shoulder or low-back disorders were analysed using binomial regression analyses and adjusted for age, sex, duration of pain and comorbidity. Results During 6 months follow-up, patients experienced clinically relevant improvements in pain, fear avoidance and psychological wellbeing. Patients with higher baseline pain and disability and who were on sickness leave were more likely to have high primary care physiotherapy utilization. Hospital contacts were predicted by higher levels of pain, disability and low psychological wellbeing. Conclusions Clinical factors and sickness leave seems to be the main predictors of primary care physiotherapy utilization, whereas for secondary care contacts, psychological factors may also be of importance. The study contributes to the on-going research into clinical pathways and may identify future target areas to reduce healthcare utilization in patients with musculoskeletal disorders.