Objective: We examined associations between the frequency of fruit and vegetable (F&V) consumption and nutritional deficiencies among Brazilian schoolchildren. Design: A cross-sectional, population-based study was performed. A short FFQ was used to assess consumption of fruits and vegetables (F&V) over the past month. The prevalence ratios (PR) and 95% confidence intervals for stunting, obesity, anaemia, vitamin A and folate deficiencies, vitamin E and vitamin D insufficiencies were estimated for low F&V consumption frequency (vegetables <= 3 times/month and fruits <= 3 times/week) and compared with children with usual F&V consumption frequency (vegetables >= 1 time/week and fruits >= 4 times/week). Setting: Acrelandia, Western Brazilian Amazon. Subjects: A total of 702 children aged 4-10 years. Results: Only 5% of children consumed F&V >= 5 times/d. Prevalence of deficiency was 31%, 15%, 9% and 2% for vitamins D, A, E and folate, respectively. Overall, 6.3% of children were anaemic, 3.3% were stunted, 2.7% were obese and 33% had multiple nutritional deficiencies. Low frequency of F&V consumption was associated with lower plasma concentrations of carotenoids and vitamin E. Nutritional deficiencies were higher among non-consumers of F&V when compared with usual consumers: anaemia (PR=1.9; 95% CI 1.0, 3.7), vitamin E insufficiency (PR=2.5; 95% CI 1.5, 4.2), vitamin D insufficiency (PR=1.5; 95% CI 1.1, 1.9) and stunting (PR=2.6; 95% CI 1.1, 6.1). Conclusions: In our study, the occurrence of nutritional deficiencies in children with low F&V consumption was twice as high as in children with usual F&V consumption, reinforcing the importance of effective actions to promote the consumption of F&V.