Background: Whiplash injuries are an important public health problem that is associated with significant disability and high health care utilization. Recent cohort studies suggest that physician care may be the most effective treatment for patients with whiplash-associated disorders. However, these findings have not been tested in a randomized controlled trial. The purpose of this study is to determine which of physician care or two rehabilitation programs of care is most effective in improving recovery of patients with recent whiplash associated disorders. Methods and Design: We designed a pragmatic randomized clinical trial. A total of 444 participants (148 in each of three arms) who reside in Southern Ontario, Canada will be recruited from a large insurer. We will include individuals who are 18 years of age or older and who are diagnosed with Grade I or II Whiplash-associated Disorders. Participants will be randomized to physician-based education and activation or one of two rehabilitation programs of care currently in use in Ontario. Our primary outcome, self-rated global recovery and all secondary outcomes (neck pain intensity, whiplash disability, health-related quality of life, depressive symptomatology and satisfaction with care) will be measured at baseline by a trial coordinator and at 6 weeks, 3, 6, 9 and 12 months follow-up by an interviewer who is blind to the participants' baseline characteristics and treatment allocation. We will also collect information on general health status, other injuries, comorbidities, expectation of recovery, work status, pain coping, legal representation, and co-interventions. The primary intention-to-treat analysis will compare time to recovery between the three interventions. This trial will have 90% power at an alpha of 0.05 to detect a 20% difference in the rate of perceived recovery at one year. Secondary analyses will compare the health outcomes, rate of recurrence and the rate of adverse events between intervention groups. Conclusion: The results of this study will provide the public, clinicians and policy makers much needed evidence on the effectiveness of common approaches used to manage whiplash-associated disorders. © 2008 Côté et al; licensee BioMed Central Ltd.