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: Acrelândia, 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.