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Background: The Fit for School (FIT) programme integrates school health and Water, Sanitation and Hygiene interventions, which are implemented by the Ministries of Education in four Southeast Asian countries. This paper describes the findings of a Health Outcome Study, which aimed to assess the two-year effect of the FIT programme on the parasitological, weight, and oral health status of children attending schools implementing the programme in Cambodia, Indonesia and Lao PDR.Methods: The study was a non-randomized clustered controlled trial with a follow-up period of two years. The intervention group consisted of children attending public elementary schools implementing the FIT programme, including daily group handwashing with soap and toothbrushing with fluoride toothpaste, biannual school-based deworming; as well as construction of group handwashing facilities. Control schools implemented the regular government health education curriculum and biannual deworming. Per school, a random selection of six to seven-year-old grade-one students was drawn. Data on parasitological infections, anthropometric measurements, dental caries, odontogenic infections and sociodemographic characteristics were collected at baseline and at follow-up (24 months later). Data were analysed using the χ2-test, Mann Whitney U-test and multilevel logistic and linear regression.Results: A total of 1847 children (mean age = 6.7 years, range 6.0-8.0 years) participated in the baseline survey. Of these, 1499 children were available for follow-up examination - 478, 486 and 535 children in Cambodia, Indonesia and Lao PDR, respectively. In all three countries, children in intervention schools had a lower increment in the number of decayed, missing and filled permanent teeth between baseline and follow-up, in comparison to children in controls schools. The preventive fraction was 24% at average. The prevalence of soil-transmitted helminth infection (which was unexpectedly low at baseline), the prevalence of thinness and the prevalence of odontogenic infections did not significantly differ between baseline and follow-up, nor between intervention and control schools.Conclusions: The study found that the FIT programme significantly contributed to the prevention of dental caries in children. This study describes the challenges, learnings and, moreover, the importance of conducting real-life implementation research to evaluate health programmes to transform school settings into healthy learning environments for children. The study is retrospectively registered with the German Clinical Trials Register, University of Freiburg (Trial registration number: DRKS00004485, date of registration: 26th of February, 2013). [ABSTRACT FROM AUTHOR]