The purpose of this study was to estimate the usual intake distribution of calcium and vitamin B(1) of fifth-grade children based on a 3-d dietary survey and to assess nutrient intake using Dietary Reference Intakes (DRIs 2010). A cross-sectional study was undertaken from October 2007 to February 2008 in schools located in Tokyo and Okayama, Japan. A total of 94 fifth-grade children attending 5 elementary schools participated in the study. The weighed plate waste method and observation were used to collect data on the school lunches and dietary records by children, accompanied by photographs used to collect data on meals at home. The study lasted 3 d, 2 non-consecutive days with school lunches and 1 d without. The estimated proportion of subjects below the Estimated Average Requirement (EAR) for calcium intake with milk in the school lunch decreased by 40% compared to the calcium intake without milk in the school lunch. Vitamin B1 intake from less than 0.45 mg/1,000 kcal fortified rice was estimated to be 0%. The intake distribution of calcium has increased by 150 mg by taking milk and the intake distribution of vitamin B1 has increased 0.20 mg by taking fortified rice in the school lunch. Calcium and vitamin B1 intake in the school lunch has changed the distribution of calcium and vitamin B1 intake upward, and decreased the number of estimated subjects that were below EAR. However, the distribution was not shifted across the board and the shape of the distribution has changed.