When compared to children from the general population, sexually abused children receive more medical services, both for physical and mental health problems. However, possible differences between sexually abused boys and girls remain unknown. The lack of control group in studies that find gender differences also prevents from determining if the differences are specific to sexual abuse or to gender. The objective of the study was to assess differences in physical and mental health between sexually abused boys and girls in comparison to those from the general population. Administrative databases were used to document physical and mental health problems of 222 males and 660 females with a substantiated report of sexual abuse between 2001 and 2010. A comparison group individually matched to those from the sexually abused group on gender, age and geographic area was also used to document gender differences in the general population. Yearly incidence rates of diagnoses resulting from medical consultations and hospitalizations of males and females were compared over five years after a first substantiated sexual abuse report using the mixed general linear model. Sexually abused girls were up to 2.2 times more likely to consult a physician than sexually abused boys for physical health problems. Similar findings are observed in the general population. Conversely, results revealed that sexually abused boys were up to 2.3 times more likely than females to consult a physician for mental health problems. This gender difference was not apparent in the general population group.