In the present study we compared comprehensive education systems and education systems using between-school tracking with regard to disparities in the quality of student-teacher relations between low and high achieving students, between students with different socioeconomic backgrounds, and between schools with different achievement and social compositions. Data from 271,760 students in 10,125 schools in 40 of the 41 education systems that participated in the Programme for International Student Assessment 2003 was analysed using three-level regression models. The results document differences between comprehensive education systems and those using between-school tracking: In the former, but not the latter, high achievers and students with higher socioeconomic backgrounds had better student-teacher relations than their schoolmates. In education systems with between-school tracking, but not in comprehensive education systems, the quality of student-teacher relations was higher in schools with a disadvantaged social composition. These findings indicate a need to develop better strategies to address the socio-emotional needs of disadvantaged students in comprehensive education systems.