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Background Low back pain (LBP) is a major cause of disability throughout the world. However, longitudinal evidence to relate low back pain and functional limitations is mostly confined to Western countries. In this study, we investigate the associations between low back pain and functional limitations in a prospective cohort of Thai adults. Methods We analysed information from the Thai Cohort Study of adult Open University adults which included 42,785 participants in both 2009 and 2013, with the majority aged 30 to 65 years and residing nationwide. We used multivariate logistic regression to explore the longitudinal associations between LBP in 2009 and 2013 (‘never’: no LBP in 2009 or 2013; ‘reverting’: LBP in 2009 but not in 2013; ‘incident’: no LBP in 2009 but LBP in 2013; and ‘chronic’: reporting LBP at both time points) and the outcome of functional limitations relating to Activities of Daily Living (ADL) in 2013. Results Low back pain was common with 30% of cohort members reporting low back pain in both 2009 and 2013 (‘chronic LBP’). The ‘chronic LBP’ group was more likely than the ‘never’ back pain group to report functional limitations in 2013: adjusted odds ratios 1.60 [95% Confidence Interval: 1.38–1.85] for difficulties getting dressed; 1.98 [1.71–2.30] for walking; 2.02 [1.71–2.39] for climbing stairs; and 3.80 [3.38–4.27] for bending/kneeling. Those with ‘incident LBP’ or ‘reverting LBP’ both had increased odds of functional limitations in 2013 but the odds were not generally as high. Conclusions Our nationwide data from Thailand suggests that LBP is a frequent public health problem among economically productive age groups with adverse effects on the activities of daily living. This study adds to the limited longitudinal evidence on the substantial impact of low back pain in Southeast Asia. Electronic supplementary material The online version of this article (doi:10.1186/s12891-016-1380-5) contains supplementary material, which is available to authorized users.