School factors associated with health-related fitness, using the National Children and Youth Fitness Survey II (NCYFS II) data, have been examined by Pate and Ross (1987), but the hierarchical structure of the data was ignored in the data analyses. The purpose of this study was to reanalyze the NCYFS II data using the hierarchical linear model and reexamine the effects of school physical education (PE) and other factors on children's 1-mile run/walk performance. Only two of five "significant" school factors were confirmed by this study, suggesting that heightened probabilities of Type I errors might have occurred in the previous study. Two confirmed key characteristics of school PE programs that led to improvement of children's cardiovascular endurance were PE specialists and the administration of fitness tests. For a hierarchical data structure, both experimental and observational units should be considered in the data analysis. The hierarchical linear model, which not only provides more accurate individual prediction but also takes group effect into account, proved to be an appropriate analytical model in analyzing the hierarchical data.