BACKGROUND: Headache, anxiety and depression are major disorders of the brain in terms of their prevalence and the burdens and costs they impose on society. Nationwide population-based studies of these disorders are necessary to inform health policy but, in research-naïve and resource-poor countries such as Nepal, a host of methodological problems are encountered: cultural, geographic, logistic and philosophical. METHODS: Expert consensus was sought among researchers from different professional and cultural backgrounds in planning and conceptualizing an epidemiological study and adapting established methods to the special situation and circumstances of Nepal. RESULTS: The methodological problems were sorted into different themes: study design; climate; geography, access and transport; sociocultural issues; safety of interviewers. Each of these was dealt with separately, and their inter-relationships explored, in finding solutions that were sometimes pragmatic. A cross-sectional questionnaire-based study, with teams of interviewers visiting households across the three physiographic divisions (with extremes in altitude) in each of the five development regions of the country, would enable national sampling with sociocultural representativeness. However, the study instruments and interviews would be in Nepali only. Transport and access challenges were considerable, and their solutions combined travel by air, bus, river and foot, with allowances for rain-damaged roads, collapsed bridges and cancelled scheduled flights. The monsoon would render many routes impassable, and therefore set an absolute time limitation. Engaging participants willingly in the enquiry would be the key to success, and several tactics would be employed to enhance the success of this, most importantly enlisting the support of local community volunteers in each study site. CONCLUSION: Anticipating problems in advance of investing substantial resources in a large nationwide epidemiological study in Nepal was a sensible precaution. The difficulties could be resolved or circumvented without expected compromise in scientific quality. Expert consensus was an effective means of achieving this outcome.