The purpose of the present study was to investigate the relationships between gender stereotypes and preferences of musical instruments among Japanese children. A survey was conducted to 338 elementary school children in the forth and sixth grades (175 boys and 163 girls). Many of the children regarded drums, guitar, and trumpet as “instrument for boys”, whereas harp, piano, and flute as “instrument for girls”. Preferences significantly differed between the boys and the girls. The boys preferred guitar and drums more than did the girls, and the girls preferred flute and harp more than did the boys. The boys tended to prefer the instruments regarded traditionally as “masculine,” whereas the girls tended to prefer those considered “feminine.” The results show that children's preferences of instruments reflect the gender stereotypes of musical instruments. Some practical ideas were suggested to neutralize gender stereotypes in classroom music instruction.