An examination of changes in children's motivation and achievement behaviors over time represents a valuable endeavor in the journey to an understanding of how motivational processes evolve in children in the domain of physical activity. Therefore, the present study examined how children's motivation and performance changed longitudinally in required running programs conducted during their regularly scheduled physical education classes.  Specifically, guided by the expectancy-value model of achievement choice (Eccles, 1998), this study examined whether mean levels of children's expectancy beliefs, subjective task values, intention for future participation in running, and their running performance changed from fourth to six grades and differed by gender.  Participants (N = 90; 53 boys; 37 girls) completed a timed mile run and questionnaires four times over a three-year period:  twice in the fourth grade (September and May), and again at the end of the fifth and sixth grades respectively.  During the study, students changed school campuses between the fourth and fifth grade. The 13-item, 5-point scale questionnaire, adapted from previous work with elementary children, assessed children's expectancy beliefs, subjective task values, and intention for future participation. The mile run was used to assess the children's running performance.  A repeated measures multivariate analysis of variance yielded a significant main effect for time, Wilks' l = .144, F (12, 77) = 38.05, p = <.001 and no significant effect for gender. Univariate analyses revealed that a significant time effect (p = <.001) existed on children's subjective task values, intention for future participation, and running performance but not for children's expectancy beliefs.  Specifically, children's subjective task values decreased across the fourth and fifth grades with no change in the sixth grade. Children's intention for future participation in running also decreased across the fourth and fifth grades but increased by the end of the sixth grade.  Lastly, children's mile run times consistently improved across all three grades. Overall, results of this study provide empirical evidence that the negative effects of the school transition on children's motivation measures observed in the classroom (Anderman, Maehr, & Midgley, 1999) also exist in the context of physical activity. Therefore, we recommend that teachers be aware of those negative effects on students' motivation in physical activity settings and work with researchers to find ways to help students minimize the effects when they move from elementary to intermediate or middle schools.