IntroductionAn increasing number of studies have found that girls in low-income settings miss or struggle at school during menstruation if they are unable to manage their menstrual hygiene effectively. This study explores the menstrual hygiene practices and knowledge of girls at rural government primary schools in the Rukungiri district in Uganda and assesses the extent to which poor menstrual hygiene management (MHM) affects their education.MethodsA self-administered questionnaire was completed by schoolgirls in six government-run primary schools in the Rukungiri district. Focus groups were held with girls from each school and semi-structured interviews were conducted with headteachers and female teachers from the participating schools. A toilet assessment was also conducted in each school.ResultsOne hundred and forty schoolgirls completed the questionnaire. The girls reported a lack of access to adequate resources, facilities and accurate information to manage their menstrual hygiene effectively at school. They reported that, as a result, during menstruation they often struggle at school or miss school. Eighty-six girls (61.7%) reported missing school each month for menstrual-related reasons (mean 1.64, range 0-10, SD. 1.84).ConclusionIt is common for girls who attend government-run primary schools in the Rukungiri district to miss school or struggle in lessons during menstruation because they do not have access to the resources, facilities, or information they need to manage for effective MHM. This is likely to have detrimental effects on their education and future prospects. A large-scale study is needed to explore the extent of this issue.