In 2009 competent organisations in the European Union provided the European Food Safety Authority (EFSA) with data from the most recent national dietary survey at the level of individuals' consumption. Twenty different Member States provided EFSA with data from 22 different national dietary surveys, with consumption figures for adults and, when available, for children. Member States' dietary data were assembled into the EFSA Comprehensive European Food Consumption Database. In this paper an overview of the methodologies and protocols employed in the different national dietary surveys is provided. Specifically, details about dietary assessment methods, interview administration, sampling design, portion size estimation, dietary software, evaluation of under-reporting and non-dietary information collected are described. This information is crucial to evaluate the level of accuracy of food consumption data and to anticipate and acknowledge the utmost important sources of heterogeneity of national databases included in the Comprehensive Database. The Comprehensive Database constitutes a unique resource for the estimation of consumption figures across the European Union and represents a useful tool to assess dietary exposure to hazardous substances and nutrient intake in Europe. Nevertheless, the many substantial methodological differences that characterise the Comprehensive Database are acknowledged and critically discussed.