The aim of this study is to analyze the gender differences in injuries at Finnish comprehensive schools. Nine schools reported a total of 1135 injuries to the injury register over two school years. Boys (56%) were injured more often than girls, their injuries happened more often during breaks at school yard, whereas girls hurt themselves during sport lectures in the gymnastic halls. The proportion of boys' injuries also increased with age. More often, boys' injuries were caused by intentional actions by other pupils. Girls injured their lower extremities more often, whereas boys injured their faces and head. Boys also suffered concussion more often than girls, and were also referred for further care to health care centres or hospitals more often than girls. The higher injury frequency among boys at school corresponds to the higher injury rate of males in general, which is true for work, traffic, and leisure-time injuries. Increased adult supervisor control especially during breaks can prevent most of school injuries.