In recent years, a number of health issues among adolescents in Japan have become highlighted. One of the major issues in school health is thinness among high school girls. Thinness is closely related to low energy intake, which can lead to menstrual dysfunction and low bone density. It is important to acknowledge these issues as health disorders that are specific to girls, and to consider measures for their prevention. The purpose of this study was to clarify the current situation of health disorders specific to high school girls, and to examine their level of awareness about them. Between March 2018 and February 2019, we conducted a self-administered questionnaire survey targeting 1,551 high school girls from 10th to 12th grade in 32 schools across 7 prefectures. This revealed that 18.7% of the girls were classified as “thin” based on Body Mass Index. In addition, many girls (more than half) had one or more signs of low energy intake, menstrual dysfunction, and history of stress fracture. The survey indicated signs of health disorders specific female high school students, suggesting that this is an important issue that needs to be addressed. The results also indicated that knowledge regarding health disorders was insufficient, as the overall correct answer rate was 50% or less. This was partly related to the presence or absence of health disorders specific to girls. In the future, it will be necessary to clarify the relevant factors that ought to be considered for comprehensive education designed to prevent health disorders specific to girls.