Background: Musculoskeletal complaints are frequent and have large consequences for public health. Information about the prognosis after presentation in general practice is far from complete. Knowledge about determinants of the clinical course of musculoskeletal complaints is essential for management decisions and to inform patients about their prognosis. The purpose of this study is to provide information about the prognosis of musculoskeletal complaints other than low back pain by studying the course of these complaints in general practice and to identify determinants of this course. Methods: Patients of 18 years and older, who present in general practice with a new episode of a musculoskeletal complaint of the neck, shoulder, elbow, wrist, hand, arm, hip, knee, ankle or foot, are recruited by their general practitioner (GP). Participants will receive complaint-specific questionnaires by mail at baseline and after 3, 6, 12 and 18 months. The following putative determinants of the course of the complaints will be investigated: sociodemographic characteristics, characteristics of the complaint, psychosocial job characteristics, physical workload, physical activity during leisure time, pain coping, mood, kinesiophobia, social support, optimism. The primary outcomes are perceived recovery, pain, functional status, sick leave and overall quality of life.