This analysis of data from three surveys between 2001 and 2012 aimed to describe indicators of wellbeing and health of secondary school students in New Zealand. Significant reductions (adjusted OR) between 2001 and 2012 were reported for cigarette use (0.27; 95% CI 0.23-0.32), alcohol use (0.39; 95% CI 0.33-0.46), marijuana use (0.37; 95% CI 0.31-0.43), sexual abuse (0.52; 95% CI 0.46-0.58), fighting (0.63; 95% CI 0.55-0.73), seatbelt use (1.47; 95% CI 1.31-1.65) and risky driving behaviours (0.39; 95% CI 0.33-0.45). There were also improvements (adjusted OR) in positive connections to school for variables including the perception that the school cares (1.22; 95% CI 1.10-1.35), liking school (1.55; 95% CI 1.33-1.82) and good family relationships (1.83; 95% CI 1.70-1.97). Parameters that failed to improve and were poor in comparison with international estimates were condom use at last sexual intercourse (adjusted OR 0.77; 95% CI 0.68-0.87), daily physical activity (0.88; 95% CI 0.78-0.99) and being overweight/obese (1.09; 95% CI 0.92-1.31). Other indicators that did not improve were exposure to family violence (adjusted OR 1.37; 95% CI 1.11-1.68) and depressive symptoms (1.03; 95% CI 0.91-1.17).