Background: Clinical guidelines generally portray acute low back pain as a benign and self-limiting condition. However, evidence about the clinical course of acute low back pain is contradictory and the risk of subsequently developing chronic low back pain remains uncertain. There are few high quality prognosis studies and none that have measured pain, disability and return to work over a 12 month period. This study aims to provide the first estimates of the one year prognosis of acute low back pain (pain of less than 2 weeks duration) in patients consulting primary care practitioners. A secondary aim is to identify factors that are associated with the prognosis of low back pain. Methods/Design: The study is a prospective inception cohort study. Consecutive patients consulting general medical practitioners, physiotherapists and chiropractors in the Sydney metropolitan region will complete a baseline questionnaire regarding their back pain. Subsequently these patients will be followed up by telephone 6 weeks, 3 months and 12 months after the initial consultation. Patients will be considered to have recovered from the episode of back pain if they have no pain and no limitation of activity, and have returned to pre-injury work status. Life tables will be generated to determine the one year prognosis of acute low back pain. Prognostic factors will be assessed using Cox regression. Discussion: This study will provide the first estimates of the one year prognosis of acute low back pain in a representative sample of primary care patients.