BACKGROUND: Musculoskeletal impairment (MSI) is an important cause of morbidity and mortality worldwide, especially in developing countries. Prevalence studies for MSI in the developing world have used varying methodologies and are seldom directly comparable. This study aimed to develop a new tool to screen for and diagnose MSI and to pilot test the methodology for a national survey in Rwanda. METHODS: A 7 question screening tool to identify cases of MSI was developed through literature review and discussions with healthcare professionals. To validate the tool, trained rehabilitation technicians screened 93 previously identified gold standard 'cases' and 86 'non cases'. Sensitivity, specificity and positive predictive value were calculated. A standardised examination protocol was developed to determine the aetiology and diagnosis of MSI for those who fail the screening test. For the national survey in Rwanda, multistage cluster random sampling, with probability proportional to size procedures will be used for selection of a cross-sectional, nationally representative sample of the population. Households to be surveyed will be chosen through compact segment sampling and all individuals within chosen households will be screened. A pilot survey of 680 individuals was conducted using the protocol. RESULTS: : The screening tool demonstrated 99% sensitivity and 97% specificity for MSI, and a positive predictive value of 98%. During the pilot study 468 out of 680 eligible subjects (69%) were screened. 45 diagnoses were identified in 38 persons who were cases of MSI. The subjects were grouped into categories based on diagnostic subgroups of congenital (1), traumatic (17), infective (2) neurological (6) and other acquired(19). They were also separated into mild (42.1%), moderate (42.1%) and severe (15.8%) cases, using an operational definition derived from the World Health Organisation's International Classification of Functioning, Disability and Health. CONCLUSION: : The screening tool had good sensitivity and specificity and was appropriate for use in a national survey. The pilot study showed that the survey protocol was appropriate for measuring the prevalence of MSI in Rwanda. This survey is an important step to building a sound epidemiological understanding of MSI, to enable appropriate health service planning.