Aims: Insomnia is a large health problem. In some prior studies, positive associations between insomnia symptoms and sickness absence have been observed. There is, however, no previous nationwide cohort study of clinically diagnosed insomnia and risk of incident sickness absence. Methods: Prospective nationwide cohort study based on Swedish population-based registers including all 4,956,358 individuals registered as living in Sweden on 31 December 2004/2005, aged 17–64 years, not on disability pension, old-age pension or on-going sickness absence. Those having insomnia inpatient or outpatient care, defined as having at least one admission/specialist visit with a main or secondary diagnosis of disorders of initiating and maintaining sleep [insomnias] (ICD-10: G47.0) during 2000/2001–2005, were compared to those with no such care. All-cause and diagnosis-specific incident sickness absence were followed during 2006–2010. Incidence rate ratios (IRRs) and 95% confidence intervals (CIs) were estimated by Cox proportional hazards regression. Results: In models adjusted for prior sickness absence, socio-demographic factors and inpatient and specialized outpatient care, associations between insomnia and increased risks of all-cause sickness absence (IRR 1.18, 95% CI 1.04–1.35) and sickness absence due to mental diagnoses (IRR 1.75, 95% CI 1.36–2.25) were observed. After further adjustment for insomnia medications these associations disappeared. No associations between insomnia and risk of sickness absence due to cancer, circulatory or musculoskeletal diagnoses, or injuries, were observed. Conclusions: In this nationwide cohort study, we observed increased risks of all-cause sickness absence and sickness absence due to mental diagnoses after adjustment for several potential confounders that disappeared after further adjustment for insomnia medications.