The Education (Scotland) Act 1872 offered the different Christian denominational schools the opportunity to transfer their schools and become non-denominational Board schools. This option was rejected by the Catholic and Episcopal churches. There were serious anxieties about issues such as the loss of denominational status and the proposal that religious instruction and observance was confined to the beginning and/or end of the school day to facilitate the conscience clause. Retaining the schools was a courageous move especially as there were very serious financial implications in the continued support for school buildings, resources and teacher salaries. There were many serious challenges for the teachers, pupils, parents and congregations (providing funds for the schools) that are addressed in the article. This article provides an examination of the Catholic and Episcopal schools in the lead up to the act, the reaction of the two churches to the Act and the consequences of the non-transfer of the schools.