Background: Musculoskeletal disorders (MSD) are multifactorial requiring multidisciplinary treatment including physiotherapy. General practitioners (GP) have a central role in managing MSDs and mostly solicit physiotherapists accounting for 76.1% of physiotherapy prescriptions in France. Patient, physician, and contextual factors, including healthcare accessibility, can influence physiotherapy prescription rates. Objective : To identify patient, physician, and contextual factors associated with physiotherapy prescription in adult patients with MSDs in general practice. Methods: This study is based on the 2011/2012 French cross-sectional ECOGEN study. Analyses included working-age patients consulting their GP for any MSD. Physiotherapy prescription was assessed initially, then adjusted multilevel logistic model analysis of patient, physician, geographical area-related factors associated with these prescriptions was performed. Results: Among the 2305 patients included, 456 (19.8%) were prescribed physiotherapy. Following multilevel multivariate analyses, physiotherapy was prescribed more frequently for female patients (OR 1.28; 95% CI [1.03, 1.59]) with spinal (OR 1.47; 95% CI [1.18, 1.83]) and upper limb disorders (OR 1.66; 95% CI [1.20, 2.29]), and less frequently for patients > 50 years (OR 0.69; 95% CI [0.52, 0.91]), living in deprived geographical areas (OR 0.60; 95% CI [0.40, 0.90]). GPs prescribed physiotherapy less frequently if they were > 50 years (OR 0.50; 95% CI [0.39, 0.63]), had a high number of annual consultations, or were practicing in semi-urban area in a multidisciplinary team. Conclusion: This multilevel analysis identifies factors associated with physiotherapy prescription for patients with MSDs, including living in deprived geographical areas. This constitutes an original contribution towards addressing healthcare disparities.