Headache is a symptom experienced by many individuals throughout life. It is a complex, multidimensional construct that, for the purpose of diagnosis, relies on the subjective symptom descriptions of those affected. The classification of headaches is influenced by the frequency of the respective pain as well as the different pain qualities and their perception. In the classification of headache, a number of different methodological problems arise that influence the estimation of prevalence and incidence rates of single headache types. The aim of this manuscript is (a) to describe and discuss the methodological problems in the assessment and classification of headache in general and single headache disorders in detail and (b) to summarize their frequency in studies of the German adult population. Cross-sectional and prospective cohort studies that assessed headache in general or the prevalence and incidence rates of single headache disorders in Germany are described and methodological problems of the assessment are discussed. The application of different methods, especially in the classification of the most frequent primary headache disorders--migraine and tension-type headache--hinders the comparability of published studies. There is a clear lack of prospective cohort studies that allow a classification of single headache disorders. Given the high frequency and considerable consequences of headache disorders in Germany, only a few studies report results on the prevalence and/or incidence rates, risk factors, and individual as well as economic consequences of different headache disorders. Methodological problems in the assessment and classification of single headache disorders have contributed to this situation. Further standardization of methods in future studies is necessary.