Objective To analyze the factors associated with the consumption of extra institutional foods and the food preferences of full-time students. Methods A cross-sectional study with students from full-time municipal schools in the city of Goiânia, Brazil, from 6 to 14 years of age, both sexes and without food restrictions. The per capita family income, maternal education, nutritional status, the consumption of extra institutional foods (meals not provided by the school) in each meal and their source, and foods with higher or lower preference in school eating habits were verified. Both a Chi-Square and a Linear Trend tests were used to analyze the data. Results Three hundred and fifty nine students participated, most of them aged between 6 and 10. More than one third consumed extra institutional foods (44.0%), with the highest frequency of consumption during the mid-morning snack (34.0%). These foods mainly originated from their own households (48.7%) and one of the main items consumed was carton juice. There was an association between adolescents and mothers with higher education levels and the consumption of these items during lunch, and between students who are non-overweight and their consumption in the afternoon snack. The preferred foods were chocolate milk and bread with butter/margarine, rice and beans, passion fruit juice, and bread with cheese/requeijão and less preferably: caramelized milk and salt biscuit, beans and beets, coconut porridge and bread with cheese. Conclusion There was a high frequency of extra institutional food consumption, associated to the age group, to a higher educational level of the mother and students who are non-overweight. Foods of higher and lower preference included dairy foods and beans.