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Objective Night work is associated with increased risk of disease, but it is unclear if it is associated with sickness absence. The aim of the study was to examine if working at night is associated with higher risk of sickness absence compared to daytime work. Methods Data was retrieved from the Danish Working Hour Database (DWHD) that includes administrative payroll data from the five Danish administrative regions in the period 2007–2013. The database includes 249,218 unique participants with 224,485,710 observations of individual working hours with daily information on starting and ending times for each shift and sickness absence. For this exploratory study we selected a single hospital in 2009 with 6,254 unique participants, 1,461,690 observations, 83% women, mean-age 40.8 years (SD = 11.9 years). Night shifts were defined as one or more shifts of at least three hours of work between 24:00 and 05:00 during the past 28 days. The reference was dayshift (at least 3 hours between 06:00–20:00). A multi-state model analysed the recurrent transitions between three states: work, sickness absence and temporary out e.g. holiday. Hazard ratios (HR) for sickness absence were calculated by Cox proportional hazards models adjusted for age and sex. Results Analyses showed that working night shifts were associated with higher risk of transitioning from work to sickness absence of any length (HR: 1.25, 95% CI: 1.12–1.4), of 1–2 days (HR: 1.21, 95% CI: 1.07–1.36), 3–4 days (HR: 1.28, 95% CI: 1.09–1.50), 5–6 days (HR: 1.67, 95% CI: 1.25–2.22), 6–7 days (HR: 2.03, 95% CI: 1.24–3.32), but not >9 days (HR: 1.21, 95% CI: 0.84–1.74) compared to day shifts. Conclusion Working at night is associated with an increased risk of short-term sickness absence compared to daytime work. Results need to be confirmed in a larger study which is on-going.