Background: Traditionally, the socio-economic position of adolescents has been measured using information about parents' occupation, parents' level of education, or household income. Since the adolescence is a developmental stage characterised by a search for and a move into individual life tracks a shift of focus from socio-economic position of origin to socio-economic position of destination is justified. Academic orientation may be used as a rough indicator of future social position. The purpose of the study was to elucidate the link between academic orientation and parents' education on the one hand and subjective health and health-related behaviour among adolescents on the other. Methods: The study was based on cross-sectional questionnaire data collected in 1999 and 2003 among 1828 18-year-old students in year 2 of upper secondary school in a Swedish city. The data were analysed using contingency tables and logistic regression. Results: Subjective health and health-related behaviour was strongly linked to academic orientation but not directly to parents' education. The pattern is unambiguous, poor health and health-damaging behaviour being significantly higher among students in non-theoretical programmes than among students in theoretical programmes. Conclusion: Academic orientation is a useful concept in order to detect health inequalities and a powerful way of identifying adolescents at higher risk. The unequal distribution of health and health-damaging behaviour according to academic orientation among adolescents turns out to be an important challenge for public health work.