Summary Objective To explore safety for girls in schools, particularly how girls perceive and negotiate dangers and risks associated with the use of toilets. Methods Participatory action research over a period of 3 days at three schools in South Africa. Informants were 81 girls 16 years and older, teachers and other relevant school personnel. Data were collected through focus group discussions, in-depth interviews, participant observation, mapping and photography. Results Toilets had inadequate or no sanitation. Both their use and their avoidance were risky for female students and discouraged hygienic practices. Experience of sexual violence from male students and teachers was a major theme, but unrelated to school toilets. Male teachers used various strategies and opportunities to gain sexual access to the girls and previous experience of victimization prevented the girls from reporting them. Conclusion To ensure a healthy school environment that promotes gender equality, all threats to safety, including the physical and social environment, must be considered.