Abstract Objective To develop and integrate the assessment of functional foods (FuF; manufactured foods with altered composition carrying a health claim) consumption into an existing risk factor surveillance system. Design FuF market research followed by an experimental FuF intake study incorporated into an ongoing community-based survey. Concurrent completion of a self-administered semi-quantitative FFQ and a self-administered, qualitative FuF frequency questionnaire (FuFFQ) followed by a face-to-face control step using FuF photographs and combined food group-based data analyses. Setting ‘Bus Santé' risk factor surveillance programme, Geneva/Switzerland. Subjects Population-based random sample of 639 residents (52 % women, aged 35-74 years) surveyed from September 2003 to April 2004. Results Local Geneva/French neighbourhood market research identified 148 FuF in five major FuF food groups which were compiled into a functional ingredient database. Prior to the face-to-face verification, 210 (33 %) individuals categorized themselves as FuF consumers, 429 (67 %) as non-consumers. The control step revealed that 70 % of the 639 participants were already familiar with the FuF concept, and thus were correctly self-categorized as FuF consumers or non-consumers. For the remaining 30 % of participants the true FuF consumption status was established, resulting in a final number of 285 FuF consumers (45 %; 12 % net increase) and 354 (55 %) non-consumers. Conclusions The developed self-administered, brief, qualitative food group-based FuF frequency check list in combination with an FFQ and a photo-assisted control step provides a flexible assessment tool for measuring FuF consumption in the context of a specific fluctuating FuF market and may be applicable to other population settings and time