The effect of physical activity on neck and low back pain is still controversial. No systematic review has been conducted on the association between daily physical activity and neck and low back pain. The objective of this study was to evaluate the association between physical activity and the incidence/prevalence of neck and low back pain. Publications were systematically searched from 1980 to June 2009 in several databases. The following key words were used: neck pain, back pain, physical activity, leisure time activity, daily activity, everyday activity, lifestyle activity, sedentary, and physical inactivity. A hand search of relevant journals was also carried out. Relevant studies were retrieved and assessed for methodological quality by two independent reviewers. The strength of the evidence was based on methodological quality and consistency of the results. Seventeen studies were included in this review, of which 13 were rated as high-quality studies. Of high-quality studies, there was limited evidence for no association between physical activity and neck pain in workers and strong evidence for no association in school children. Conflicting evidence was found for the association between physical activity and low back pain in both general population and school children. Literature with respect to the effect of physical activity on neck and low back pain was too heterogeneous and more research is needed before any final conclusion can be reached.