Background: Previous studies have shown evidence of comorbid conditions in chronic fatigue syndrome/myalgic encephalomyelitis (CFSIME). Objective: To estimate the prevalence of comorbidities and assess their associations using a nationwide population-based database of a Spanish CFSIME cohort. Method: A nationally representative, retrospective, cross-sectional cohort study (2008-2015) assessed 1757 Spanish subjects who met both the 1994 Centers for Disease Control and PreventionlFukuda definition and 2003 Canadian Criteria for CFSIME. Socio-demographic and clinical data, comorbidities, and patient reported outcome measures at baseline were recorded A cluster analysis based on baseline clinical variables was performed to classify patients with CFSIME into 5 categories according to comorbidities. A multivariate logistic regression analysis was conducted adjusting for potential confounding effects such as age and sex; response and categorical predictor variables were also assessed Results: A total of 1757 CFSIME patients completed surveys were collected We identified 5 CFSIME clusters: group 1-fibromyalgia, myofascial pain, multiple chemical hypersensitivity, sicca syndrome, epicondylitis, and thyroiditis; group 2 alterations of ligaments and subcutaneous tissue, hypovitaminosis D, psychopathology, ligamentous hyperlaxity, and endometriosis. These 2 subgroups comprised mainly older women, with low educational level, unemployment, high levels of fatigue, and poor quality of life; group 3 with hardly any comorbidities, comprising mainly younger women, university students or those already employed, with lower levels of fatigue, and better quality of life; group 4 poorly defined comorbidities; and group 5 hypercholesterolemia. Conclusion: Over 80% of a large population-based cohort of Spanish patients with CFSIME presented comorbidities. Among the 5 subgroups created, the most interesting were groups 1-3. Future research should consider multidisciplinary approaches for the management and treatment of CFSIME with comorbid conditions.