Objectives: Ehlers-Danlos syndrome (EDS) constitutes a group of connective tissue diseases with variable organ dysfunction. We aimed to examine the comorbidity burden in patients with EDS. Methods: A nationwide population-based cohort study linking data from Danish registers from the year 2000-2014. The EDS cohort was identified using the International Classification of Diseases version 10 (ICD-10) EDS code. The control cohort was formed from the Danish general population by randomly matching the EDS cohort in a ratio of 1:25 by sex and date of birth. Hospital contacts were used to identify the most frequently occurring ICD-10 codes. We investigated the frequencies of the disease categories and unique ICD-10 codes and compared these between the cohorts. Results: The EDS cohort included 1,319 patients and the control cohort 46,700 patients. All disease categories and ICD-10 codes were significantly more frequent within the EDS cohort, especially those related to common manifestations of EDS. Other comorbidities such as asthma, pneumonia, gastrointestinal functional disorders, and hernias were also significantly more common in the EDS cohort. Conclusions: The most common comorbidities in Danish patients with EDS were gastrointestinal functional disorders, hernias, asthma, pneumonia, and osteoporosis. The causality between these comorbidities and EDS should be investigated further.