Background Doctors have a low prevalence of sickness absence. Employment status is a determinant in the multifactorial background of sickness absence. The effect of doctors’ employment status on sickness absence is unexplored. The study compares the number of sickness absence days during the last 12 months and the impact of employment status, psychosocial work stress, self-rated health and demographics on sickness absence between self-employed practitioners and employed hospital doctors in Norway. Methods The study population consisted of a representative sample of 521 employed interns and consultants and 313 self-employed GPs and private practice specialists in Norway, who received postal questionnaires in 2010. The questionnaires contained items on sickness absence days during the last 12 months, employment status, demographics, self-rated health, professional autonomy and psychosocial work stress. Results 84% (95% CI 80 to 88%) of self-employed and 60% (95% CI 55 to 64%) of employed doctors reported no absence at all last year. In three multivariate logistic regression models with sickness absence as response variable, employment category was a highly significant predictor for absence vs. no absence, 1 to 3 days of absence vs. no absence and 4 to 99 days of absence vs. no absence), while in a model with 100 or more days of absence vs. no absence, there was no difference between employment categories, suggesting that serious chronic disease or injury is less dependent on employment category. Average or poor self-rated health and low professional autonomy, were also significant predictors of sickness absence, while psychosocial work stress, age and gender were not. Conclusion Self-employed GPs and private practice specialist reported lower sickness absence than employed hospital doctors. Differences in sickness compensation, and organisational and individual factors may to a certain extent explain this finding.