Long term sickness absence (LTSA) is a major public health problem. We examined the impact of four, potentially modifiable, health behaviours, such as smoking, alcohol consumption, leisure time physical activity, and the associated variable of body mass index on the risk of subsequent LTSA. This was done by following a representative population sample of 5,020 Danish employees aged 18-69 for 18 months in a national register on social transfer payments. Risk estimates for onset of LTSA and etiologic fractions were computed. In women, ex-smokers and heavy smokers had an increased risk of LTSA of 1.61 and 2.05 respectively after adjustment for age, family status, socio economic status, school education, physical and psychosocial work environment exposures and diagnosed disease. In men, effect estimates were smaller and only borderline significant in the fully-adjusted model. The etiologic fraction of smoking was 17.4% in men and 25.5% in women.