The cost of brain disorders in Denmark is unknown and such information is important to decision makers. The aims of the study were to estimate the total number of subjects with brain diseases, and the associated direct and indirect expenses in Denmark. This was part of a larger pan-European study commissioned by the European Brain Council, which is an international collaboration of organizations within psychiatry, neurology, neurosurgery, neuro-research and patient organizations. The project provided the best possible estimates of the expenses for brain diseases based on available international scientific literature. The present study presents results for Denmark. There were an estimated 1.4 million Danish citizens who in 2004 had one of the selected 12 brain diseases, equivalent to one quarter of the total population. Anxiety disorders and migraine were the two most frequent diseases with 500,000 and 340,000 patients, respectively. The total expenses for all selected brain diseases were 37.3 billion DKR. Affective disorders, dependency, dementia and stroke were the most costly diseases. An estimated 12% of all direct costs in the Danish health system were spent on brain diseases; 9% of the total drug consumption was used for treatment of brain diseases. Expenses to brain diseases constituted 3% of the gross domestic product. Brain disorders are very prevalent in Denmark and they cause high societal and personal cost.