BACKGROUND : It has been suggested that specific interventions delivered through the education sector in low- and middle-income countries might improve children's health and wellbeing. This cluster-randomised controlled trial aimed to evaluate the effects of a school garden programme and complementary nutrition, and water, sanitation and hygiene (WASH) interventions on children's health and nutritional status in two districts of Nepal. METHODS : The trial included 682 children aged 8-17 years from 12 schools. The schools were randomly allocated to one of three interventions: (a) school garden programme (SG; 4 schools, n = 172 children); (b) school garden programme with complementary WASH, health and nutrition interventions (SG+; 4 schools, n = 197 children); and (c) no specific intervention (control; 4 schools, n = 313 children). The same field and laboratory procedures were employed at the baseline (March 2015) and end-line (June 2016) surveys. Questionnaires were administered to evaluate WASH conditions at schools and households. Water quality was assessed using a Delagua kit. Dietary intake was determined using food frequency and 24-h recall questionnaire. Haemoglobin levels were measured using HemoCue digital device and used as a proxy for anaemia. Stool samples were subjected to a suite of copro-microscopic diagnostic methods for detection of intestinal protozoa and helminths. The changes in key indicators between the baseline and end-line surveys were analysed by mixed logistic and linear regression models. RESULTS : Stunting was slightly lowered in SG+ (19.9 to 18.3%; p = 0.92) and in the control (19.7 to 18.9%). Anaemia slightly decreased in SG+ (33.0 to 32.0%; p < 0.01) and markedly increased in the control (22.7 to 41.3%; p < 0.01), a minor decline was found in the control (43.9 to 42.4%). Handwashing with soap before eating strongly increased in SG+ (from 74.1 to 96.9%; p = 0.01, compared to control where only a slight increase was observed from 78.0 to 84.0%). A similar observation was made for handwashing after defecation (increase from 77.2 to 99.0% in SG+ versus 78.0 to 91.9% in control, p = 0.15). CONCLUSIONS : An integrated intervention consisting of school garden, WASH, nutrition and health components (SG+) increased children's fruit and vegetable consumption, decreased intestinal parasitic infections and improved hygiene behaviours. BACKGROUND : ISRCTN17968589 (date assigned: 17 July 2015).