OBJECTIVE: To measure factors affecting food choice in a sample of Greek schoolchildren attending 5th and 6th grade. DESIGN: Three self-administered questionnaires were distributed to the participants - one on nutritional knowledge, one on self-efficacy and social support for dietary change and a food-frequency questionnaire. SETTING: One hundred Greek primary schools from Attica and Thessaloniki regions. SUBJECTS: In total, 2439 students in 5th and 6th grades. RESULTS: Principal components analysis was applied to extract the main factors affecting food choice of our subjects. Six components were derived explaining 66% of the total variation in factors affecting food choice. The first component was characterised by readiness to make the healthier choice when competitive foods are considered (explained variation 29%); the second was characterised by the impact of parents, friends and advertisements on students' choices and also the impact of taste, smell and cooking method on the consumption of vegetables (explained variation 11%); the third component was characterised by readiness to choose fresh foods instead of ready-to-eat, pre-packaged choices as a main meal and awareness of the health value of fruits and vegetables (explained variation 8%); the other components mainly expressed the interdependence of the main factors. CONCLUSIONS: Nutrition education and health promotion programs in Greece must include family members and activities regarding food preparation, as well as education and environmental changes in schools. Public health measures must include regulation of advertising. Moreover, the categorisation of foods as 'healthier but less tasty' and 'appealing but unhealthy' needs to be challenged in the future, since balanced nutrition is founded in variety and norm.