Background: Diets abundant in fruits and vegetables are associated with reduced risk for chronic disease, but intakes of adolescents are often inadequate. To design effective interventions it is important to understand how dietary intake changes longitudinally during adolescence and to monitor progress in the population toward fruit and vegetable consumption recommendations. The objective of this study was to examine longitudinal and secular trends in fruit and vegetable intake among two cohorts of Minnesota adolescents over the period 1999-2004. Methods: Measures of fruit and vegetable intake and demographics were completed by 944 boys and 1161 girls who were Project EAT participants in 1999 and 2004. In 2005, mixed linear regression models were used to estimate (1) longitudinal trends among two cohorts of young people during developmental transitions and (2) age-matched secular trends between the two cohorts of young people at middle adolescence. Results: Longitudinal trends indicated that adolescents decreased their daily intake of fruit and vegetables by an average of 0.7 servings during the transition from early to middle adolescence and by 0.6 servings from middle to late adolescence. Analyses of age-matched secular trends at middle adolescence showed a mean daily decrease of 0.7 servings among girls and 0.4 servings among boys between 1999 and 2004. Conclusions: The large longitudinal and secular declines in fruit and vegetable intakes of adolescents indicate a strong need for further research to understand why consumption is decreasing among adolescents and to develop more effective interventions for increasing fruit and vegetable consumption during this critical developmental period.