BACKGROUND : In developed countries high socioeconomic status (SES) is associated with lower body mass index (BMI) and greater height compared with low SES. OBJECTIVE : To investigate differences in BMI/height in adolescent students from two different school types with divergent SES backgrounds. METHODS : A total of 4579 students (2313 female), aged 11-16 years, attending either low SES vocation-directed secondary schools (VSS) or high SES secondary academic schools (AHS) were compared. Potential differences were investigated using ANCOVA models including sex, school type, geographical region and degree of urbanicity. RESULTS : At all ages between 11 and 16 years the BMI of students attending VSS was significantly higher than that of students attending AHS (mean +0.87kg/m2). The AHS students were on average taller (mean +0.93cm; p<0.001), without statistically significant age-specific differences. The taller height contributed to lower BMI by approximately 25%. Short stature, overweight and obesity were 2.3-fold, 1.8-fold and 2.5-fold, respectively more frequent in VSS than in AHS students. The BMI was higher in students in Vienna than in communities with >100,000 (p<0.001) and 20,000-100,000 (p=0.045) but similar to communities with <20,000 inhabitants. CONCLUSIONS : These findings suggest that differences in BMI and height between students reflect early SES-based grouping into school types according to the academic level of the schools they attend.