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.