Abstract Background Our study aims to follow this effort and to explore the association between health, socioeconomic background, school-related factors, social support and adolescents' sense of coherence and educational aspirations among adolescents from different educational tracks and to contribute to the existing body of knowledge on the role of educational aspirations in the social reproduction of health inequalities. We expect that socioeconomic background will contribute to the development of educational aspirations, but this association will be modified by available social and individual resources, which may be particularly favourable for the group of adolescents who are on lower educational tracks, since for them such resources may lead to gaining a higher educational level. Methods We collected data on the socioeconomic background (mother's and father's education and employment status, doubts about affordability of future study), school-related factors (school atmosphere, school conditions, attitudes towards school), perceived social support, sense of coherence (manageability, comprehensibility, meaningfulness) and the self-rated health of a national sample of Slovak adolescents (n = 1992, 53.5% females, mean age 16.9 years). We assessed the association of these factors with educational aspirations, overall and by educational tracks (grammar schools, specialised secondary schools, vocational schools). Results We found statistically significant associations with educational aspirations for the factors parental educational level, father's unemployment, doubts about the affordability of future study, school atmosphere, attitude towards school, social support from the father and a sense of coherence. Social support from the mother and friends was not associated with educational aspiration, nor was self-rated health. Besides affinity towards school, the determinants of educational aspirations differed among adolescents on different educational tracks. Educational aspirations of grammar school students were associated with father's education, while the aspirations of their peers on lower educational tracks had a stronger association with mother's education and perceived social support from father and friends. Moreover, a sense of coherence contributes to the reporting of educational aspiration by students on different educational tracks. Conclusions Characteristics of the school environment, the family and the individual adolescent are all associated with the level of educational aspiration, but in a different way for different educational tracks. Interventions aimed at reducing socioeconomic inequalities in health via the educational system should, therefore, take this variation and the rather pivotal role of the father into account.