Background: Promoting young peoples mental well-being and reducing socioeconomic inequalities are priority areas for WHO and the Scottish Government. This article describes changes in the subjective health and mental well-being of adolescents living in Scotland between 1994 and 2006, and investigates socioeconomic inequalities in mental well-being and subjective health over time. Methods: Data from the 1994, 1998, 2002 and 2006 Health Behaviour in School-aged Children surveys were analysed using Multilevel Binomial modelling. Results: Boys and younger adolescents scored more favourably on measures of confidence, happiness, helplessness and feeling left out than girls and older adolescents. Multiple health complaints (MHC) were also more prevalent among girls than boys. Significant increases over time were observed for all mental well-being measures among girls and for all but confidence among boys. Similarly, there was a significant decrease in odds of MHC over time for both boys and girls. There were no socioeconomic inequalities in any of the five outcomes in 1998. However by 2006, socioeconomic inequalities in young peoples happiness, confidence and MHC emerged, while inequalities in girls helplessness also approached significance. Between 1998 and 2006 significant increases in socioeconomic inequalities in happiness and MHC were observed and increases in feeling left out also approached significance. Conclusions: Adolescent mental well-being and subjective health in Scotland is improving. However, gender differences persist and socioeconomic inequalities are emerging for some measures, suggesting that a longer term monitoring of mental well-being and subjective health in Scotland is required.