Although boys and girls are generally located in the same physical school environment, it may be experienced differently by, and have varying implications for, boys and girls. Girls like school more and achieve higher school marks, but they also perceive more school-related pressure. Based on a total sample of 8456 ninth grade pupils in Stockholm in 2004, this study uses multilevel linear regression to analyse differences between boys and girls with regard to a number of school-performance indicators (demands, motivation, teacher support and school marks) and their association with subjective health complaints. Results showed that girls perceive more demands, show greater academic motivation, perform better in school and report more emotional support from teachers than boys. In contrast, instrumental and appraisal support from teachers are more commonly reported by boys. Associations between school-performance indicators and subjective health complaints were slightly stronger for girls than for boys. Contextual variation in health complaints, especially between classes, was found only for girls. High achievement motivation and emotional teacher support in the school class was associated with better pupil health, suggesting that a positive climate in terms of motivation and support favours class health as a whole.