Roman Catholic schools have been part of the state-funded system of education in England and Wales since the 1850s. Currently, Roman Catholic schools provide places for around 10% of students attending state-maintained primary and secondary schools. The present study employed data collected during the 1990s to compare a range of religious, social, and personal values among 1,948 year 9 and year 10 students from 10 Catholic schools (between 13 and 15 years of age) with those of 20,348 students from 93 schools without a religious foundation. It builds on earlier analyses of the same database by comparing the effect of school foundation after controlling for the individual religiosity of pupils using multilevel linear modelling. The data showed that students attending Catholic schools were significantly different from students attending schools without a religious foundation, after controlling for personal, contextual, psychological and religious factors, in respect of five of the 11 dependent variables tested. Students in Catholic schools were less likely to oppose drug use, more likely to support age-related illegal behaviours, had a poorer attitude toward school, and were more likely to oppose abortion or contraception. Some of these differences were related to the greater disaffection of non-religious pupils at Catholic schools compared with their counterparts in schools without a religious foundation. These findings suggest the value of conducting a comparable study during the 2010s.