Background There are very few studies on the frequency of breakfast and snack consumption and its relation to fruit and vegetable intake. This study aims to fill that gap by exploring the relation between irregular breakfast habits and snack consumption and fruit and vegetable intake in Tuscan adolescents. Separate analyses were conducted with an emphasis on the potentially modifying factors of sex and age. Methods Data was obtained from the 2010 Tuscan sample of the Health Behaviour in School-aged Children (HBSC) study. The HBSC study is a cross-sectional survey of 11-, 13- and 15-year-old students (n = 3291), selected from a random sample of schools. Multivariate logistic regression was used for analyzing the food-frequency questionnaire. Results A significant relation was found between low fruit and vegetable intake and irregular breakfast habits. Similarly, low fruit intake was associated with irregular snack consumption, whereas vegetable intake did not prove to be directly related to irregular snack consumption. Different patterns emerged when gender and age were considered as modifying factors in the analyses. A statistically significant relation emerged only among female students for irregular breakfast habits and fruit and vegetable intake. Generally, older female participants with irregular breakfast habits demonstrated a higher risk of low fruit and vegetable intake. Age pattern varied between genders, and between fruit and vegetable consumption. Conclusions Results suggest that for those adolescents who have an irregular consumption of breakfast and snacks, fruit intake occurs with a lower frequency. Lower vegetable consumption was associated with irregular breakfast consumption. Gender and age were shown to be moderators and this indicated the importance of analyzing fruit and vegetable intake and meal types separately. This study also confirmed that health-promotion campaigns that aim to promote regular meal consumption and consumption of fruits and vegetables need to take into account gender and age differences in designing promotional strategies. Future research should identify evidence-based interventions to facilitate the achievement of the Italian guidelines for a healthy diet for fruit, vegetables and meals intake.