The purpose of this study was to examine relative validity of a food frequency questionnaire (FFQ) to measure food acculturation in young Mexican-origin children. In 2006, Spanish-speaking staff interviewed mothers in a community-based sample of households from Ventura, California (US) (n = 95) and Guanajuato, Mexico (MX) (n = 200). Data included two 24-h dietary recalls (24-DR); a 30-item FFQ; and anthropometry of the children. To measure construct, convergent, and discriminant validity, data analyses included factor analysis, Spearman correlations, t-test, respectively. Factor analysis revealed two constructs: 1) a US food pattern including hamburgers, pizza, hot dogs, fried chicken, juice, cereal, pastries, lower fat milk, quesadillas, and American cheese and 2) a MX food pattern including tortillas, fried beans, rice/noodles, whole milk, and pan dulce (sweet bread). Out of 22 food items that could be compared across the FFQ and mean 24-DRs, 17 were significantly, though weakly, correlated (highest r = 0.62, for whole milk). The mean US food pattern score was significantly higher, and the MX food pattern score, lower in US children than in MX children (p < 0.0001). After adjusting for child's age and gender; mother's education; and household size, the US food pattern score was positively related to body mass index (BMI) z-scores (beta coefficient: +0.29, p = − 0.004), whereas the MX food pattern score was negatively related to BMI z-scores (beta coefficient: −0.28, p = 0.002). This tool may be useful to evaluate nutrition education interventions to prevent childhood obesity on both sides of the border.