Performance differences can be explained by aptitude and student background, but also by the culture of the school the students attend. The degree to which socio-economic background matters for PISA achievement scores differs significantly across countries. Both TIMSS and PISA surveys concluded that in most countries the social background of a school is associated with science performance too. Schools with students of higher socio-economic status often tend to support academic learning. To investigate the relation of schools’ socio-economic compositions to the respective science performance, Estonian schools were grouped according to their socio-economic intake relative to the national average. Three categories of schools were identified. The socio-economic gradient was used as a tool to analyse the relationship between socio-economic background and student performance. Students’ actual performance in advantaged, disadvantaged and mixed schools was compared with their predicted performance based on their individual socio-economic background. The schools were sorted by the difference in observed and expected performance. In the next step, the socio-economic status differences of Estonian and Russian instruction schools was compared and examined whether there is a relationship between the school status and students’ science attitudes toward science. The results reveal a difference between different school groups and students’ attitudes.