The aim of this study was to investigate the most frequent comorbid diseases occurring in patients with cluster headache (CH) and, for comparison, in migraine patients. Over a period of eight years 130 patients with CH and 982 patients with migraine were diagnosed according to ICHD-II criteria. In all patients the presence and type of different diseases were assessed from medical records and coded by the ICD, X revision. Odds ratios (OR) with corresponding 95% confidence intervals (95% CI) were calculated by logistic regression analyses. Comorbid disorders were present in 56.9% patients with CH and in 56.7% migraine patients. Chronic sinusitis (p = 0.001), malignancy (p = 0.012), diabetes mellitus (p = 0.021), glaucoma (p = 0.038), as well as another primary headache disorders were more frequently present in patients with cluster headache (p = 0.001), than in migraine patients. In the multivariate analysis, chronic sinusitis (OR = 7.6, p = 0.001) and diabetes mellitus (OR = 4.2, p = 0.035), adjusted by gender, age and duration of headache, are more frequently associated with CH than with migraine. Comorbid disorders in CH patients were frequent and similar to those noticed in migraine patients, except chronic sinusitis and diabetes mellitus.