OBJECTIVES: To study the effects of pain on sickness absence, taking into account physical and psychosocial work load and socio-economic position. METHODS: Data consisted of City of Helsinki personnel register data on sickness absence and a cross-sectional questionnaire survey which was carried out among employees of the City of Helsinki who reached the age of 40, 45, 50, 55 or 60 years during the years 2000-2002 (n = 8960, response rate 67%). Data sets were combined for those who gave permission for such linkage (78%). The main statistical method was negative binomial regression analysis. RESULTS: The burden of pain on sickness absence was dependent on the duration of absence: the longer the duration, the higher the burden. Self-certified absence was equally predicted by acute and chronic pain, but medically certified absence was more clearly predicted by chronic pain. Adjustments for a range of work load factors and socio-economic position showed that pain was a relatively independent determinant of subsequent sickness absence, but in particular physical work load and socio-economic position explained a small proportion of the association. Overall, pain accounted for 13% of self-certified absence among women and 8% among men. Corresponding figures were 23% and 25% for medically certified 4-14-day sickness absence and 37% and 30% for absence of over 2 weeks. CONCLUSIONS: The burden of pain on medically certified sickness absence is considerable. Prevention of pain problems is vital for reducing sickness absence rates.