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The prevalence of migraine and tension-type headache (TTH) varies considerably with respect to gender, age group and geographic regions. Methodological differences in the assessment and classification of cases are a major cause of this variability across studies, limiting the ability to perform true regional comparisons. We conducted three population-based studies in different German regions and assessed headache prevalence and headache characteristics in face-to-face interviews, applying standardized methods. We analysed the 6-month prevalence of migraine, TTH and their probable subtypes based on the new criteria of the International Headache Society (IHS). Among the 7417 participants in all three regions, the pooled 6-month prevalence of migraine, probable migraine, TTH and probable TTH was 6.75, 4.40, 19.86 and 11.61%, respectively. Despite the application of standardized classification methods, regional variations between 4.39 and 8.00% for migraine and 15.44 and 23.64% for TTH were observed, indicating differences in the local headache burden. Application of the new IHS criteria yielded headache categories that were not mutually exclusive, indicating a need for further discussion about the value of probable headache types in epidemiological studies.