Background: To explore three schools based transitions and their impact on positive Self- Reported- Health (SRH), pre-school to elementary school (6–10 y), elementary school to junior high school (10-13y) and junior high school to upper secondary school/high school (13-16y), in a long-term longitudinal population based study. Methods: The study followed three cohorts through one school transition each. A longitudinal study with data from 6693 children and their Health Dialogue Questionnaires© were used. Data were collected in the middle of Sweden during 2007–2012 with school children age 6–16 years old. Results: Several significant factors were identified impacting the positive SRH among children age 6-16y; not feeling sad or depressed, afraid or worried, positive school environment (schoolyard and restrooms), not bullied, good sleep, daily physical activity and ability to concentrate. There was no single factor identified, the factors differed according to gender and age. Conclusion: The study has identified several gender and age specific factors for successful school transitions relevant for a positive SRH. This is valuable information for school staff, parents and school children and provides a possibility to provide support and assistance when needed.