School lunches serve to improve nutritional status and to promote the health of children. The purpose of this study was to investigate the portion sizes of school lunches served and consumed in Japanese elementary schools. In addition, gender difference in servings and consumption were also studied. A cross-sectional study was undertaken between October 2007 and February 2008 in schools located in Tokyo and Okayama, Japan. A total of 192 fifth-grade children attending four elementary schools participated in this study. Weighed plate waste methods and observation were used to collect dietary data for two non-consecutive days. The proportion of children who chose staple foods along with main dishes and/or side dishes for at least one day was higher in boys than in girls (respectively, for staple food: 42.1% vs. 9.3%, for main dish and/or side dish: 68.4% vs. 44.3%, P < 0.001). The ratio of initial amount served to amount offered was 0.88 ± 0.11 for boys and 0.84 ± 0.10 for girls (P < 0.05). The ratio of amount consumed to amount offered was 1.04 ± 0.19 for boys and 0.88 ± 0.12 for girls (P < 0.001). Weight was related to amount consumed both in boys (r = 0.222, P < 0.05) and in girls (r = 0.201, P < 0.05). These findings suggest that the nutritional standards of school lunch programs should take into account gender differences. Clearly, boys were more likely to consume more than the initial amounts served due to their higher propensity to take second helpings. Boys feel few reservations about taking second helpings to adjust their total intake. However, school lunch plans should take into consideration girls' reluctance to do so, by serving appropriate initial portion sizes.