Background The major disorders of the brain (MDBs), in terms of their prevalence and the burdens of ill health, disability and financial cost that they impose on individuals and society, are headache, depression and anxiety [1-4]. Tension-type headache (TTH) and migraine are the second and third most prevalent disorders in the world [5], and migraine is the seventh highest specific cause of years of life lost to disability (YLDs) [5,6]. Major depressive and anxiety disorders are not as prevalent, but still common, and they contribute even more to disability at societal level: respectively they are the second and sixth leading specific causes of YLDs [5,7]. This is the global picture, but there are quite substantial regional uncertainties. Most epidemiological studies of the MDBs have been carried out in Western Europe and North America, so that their prevalence is poorly described, or unknown, in many large and populous regions elsewhere. This is nowhere more obvious than in the South-East Asia Region (SEAR), the only one of WHO’s six world regions for which no national data have been gathered so far of the societal impact of MDBs [8]. Nepal is a country of wide sociocultural diversity, while its three physiographic divisions attest its extraordinary geographical variation: from the Terai, or flat river plain of the Ganges in the south, at an altitude of below 300 m, through the central Hill division at 800–4,000 m, to the Himalayan Mountains above 4,000 m in the north containing eight of the world’s ten highest peaks [9]. In July 2011, the country’s population was estimated at almost 30 million [9], with nearly one quarter below the international poverty line of US$ 1.25 a day [9]. In such a country, how important are these MDBs? Very limited studies in Nepal have reported headache as one of the "major physical complaints" in both psychiatric and non-psychiatric clinics [10,11]. The Global Burden of Disease study 2010 (GBD2010) could only extrapolate to Nepal, since population-based data were not available from Nepal itself, but estimated that depressive disorders and migraine were each likely to be in the top five causes of disability, and anxiety in the top 20 [12]. This represents a lot of disability, in a country where life is a struggle. Yet, as elsewhere these conditions are neglected health problems [8]. The primary objective of this study was to estimate the prevalence and burden attributed to each of anxiety, depression and the headache disorders of public-health importance (migraine, TTH and medication-overuse headache [MOH]) in Nepal. The secondary objective was to identify the factors associated with each: demographic, life-style, comorbidities and health-care resource-utilization. The purpose was to support health policy through needs assessments, and provide evidence for health-care resource allocation in Nepal.