Objective: Understanding the mechanisms linking sleep impairment to morbidity and mortality is important for future prevention, but these mechanisms are far from elucidated. We aimed to determine the relation between impaired sleep, both in terms of duration and disturbed sleep, and allostatic load (AL), which is a measure of systemic wear and tear of multiple body systems, as well as with individual risk markers within the cardiac, metabolic, anthropometric, and immune system. Methods: A cross-sectional population-based study of 5226 men and women from the Danish Copenhagen Aging and Midlife Biobank with comprehensive information on sleep duration, disturbed sleep, objective measures of an extensive range of biological risk markers, and physical conditions. Results: Long sleep (mean difference 0.23; 95% confidence interval, 0.13, 0.32) and disturbed sleep (0.14; 0.06, 0.22) were associated with higher AL as well as with high-risk levels of risk markers from the anthropometric, metabolic, and immune system. Sub-analyses suggested that the association between disturbed sleep and AL might be explained by underlying disorders. Whereas there was no association between short sleep and AL, the combination of short and disturbed sleep was associated with higher AL (0.19; 0.08, 0.30) and high-risk levels of immune system markers. Conclusion: Our study suggests small but significant differences in the distribution of allostatic load, a pre-clinical indicator of disease risk and premature death, for people with impaired relative to normal sleep. Impaired sleep may be a risk factor for developing disease and be a risk marker for underlying illness or sleep disorders.