Mental health problems in children represent a significant international health concern, with up to one in five children using mental health services during the course of any given year. Identifying the processes of what prevents social, emotional and behaviour difficulties (SEBD) and promotes healthy development from an early age can make a significant contribution to the promotion of positive mental health in children. This article describes a longitudinal study which sought to identify the risk and promotive factors as young children move from the early to junior years in primary school. Multilevel analysis was used to identify the individual, classroom, school, home and community factors that predict change in SEBD and in prosocial behaviour in the early school years. It also calculated the cumulative effect of the various risk and promotive factors on the pupils’ well-being and mental health. The article presents the windows of vulnerability and opportunity for young children’s healthy development, proposing a trajectory for healthy development in early and middle childhood.