This study evaluates the effect of Gay and Straight Alliances (GSAs) on tolerance towards homosexuality and on perceived security of gay, lesbian and bisexual (GLB) pupils in Dutch secondary schools. This study is based on quantitative analyses of large-scale interview data retrieved from the Veiligheidsmonitor (National School Safety Monitor) 2012, including data of over 8,500 pupils in 42 schools. Important other school policies concerning safety have been taken into account in the analyses. The results show that pupils at schools with a GSA are more tolerant towards homosexuality than those at schools without a GSA. In addition, GLB pupils at schools with a GSA perceive the school climate more often as gay-friendly. GSA initiatives appear to fulfill two of their three goals. No evidence has been found that GSAs also fulfill their third goal: GLB pupils are less afraid to have their coming out at a GSA-school.