A wide variety of risk factors for the occurrence and prognostic factors for persistence of non-specific musculoskeletal pain (MSP) are mentioned in the literature. A systematic review of all these factors is not available. Thus a systematic review was conducted to evaluate MSP risk factors and prognostic factors, classified according to the dimensions of the International Classification of Functioning, Disability and Health. Candidate systematic reviews were identified in electronic medical journal databases, including the articles published between January 2000 and January 2008 that employed longitudinal cohort designs. The GRADE Working Group's criteria for assessing the overall level of evidence were used to evaluate the reviews. Nine systematic reviews were included, addressing a total of 67 factors. High evidence supported increased mobility of the lumbar spine and poor job satisfaction as risk factors for low back pain. There was also high evidence for intense pain during the onset of shoulder and neck pain and being middle aged as risk factors for shoulder pain. High evidence was also found for several factors that were not prognostic factors. For whiplash-associated disorders these factors were older age, being female, having angular deformity of the neck, and having an acute psychological response. Similarly, for persistence of low back pain, high evidence was found for having fear-avoidance beliefs and meagre social support at work. For low back pain, high evidence was found for meagre social support and poor job content at work as not being risk factors.