Objective: The aim of this study was to evaluate the effects of unspecific neck pain and low back pain at a given time (1990-91) with respect to physical and social functioning and role limitations due to emotional problems 12 years later. Methods: A rural male study population (2351 individuals) was established in 1989 and a first survey conducted in 1990-91. A follow-up survey was performed in 2002-03. A total of 1405 persons participated in both surveys. Functioning and role limitations in 2002-03 were evaluated using the SF-36 instrument. Several possible confounders were included in the analyses. Results: Unspecific neck pain or low back pain in 1990-91 was shown in a multivariate longitudinal regression model to be significantly related to limited physical (odds ratio (OR) = 2.08, 95% confidence interval (CI) 1.51-2.87) and social (OR= 1.92, 95% CI 1.33-2.75) functioning 12 years later. The effects were only slightly modified by the confounders analysed. However, higher education independently and significantly predicted a low risk for functional limitations. Conclusion: Non-specific neck pain and low back pain at a given time impacted on the risk of limited physical and social functioning many years later. Current symptoms of depression and anxiety at the time for the second survey had a high impact on functional limitations. © 2008 Foundation of Rehabilitation Information.