Backround: Political and sociocultural differences between countries can affect the outcome of clinical and epidemiological studies in ALS. Cross-national studies represent the ideal process by which risk factors can be assessed using the same methodology in different geographical areas. Methods: A survey of three European countries (The Netherlands, Ireland and Italy) has been conducted in which incident ALS patients and matched controls were recruited in a population-based study based on age, gender and area of residency, under the Euro-MOTOR systems biology programme of research. Findings: We have identified strengths and limitations during the trajectory of the Euro-MOTOR study, from the research design to data analysis. We have analysed the implications of factors including cross-national differences in healthcare systems, sample size, types of matching, the definition of exposures and statistical analysis. Conclusions: Addressing critical methodological aspects of the design of the Euro-MOTOR project minimises bias and will facilitate scientific assessment of the independent role of well-defined exposures.