BACKGROUND: In 2008, the Irish Government initiated a pilot Healthy Schools Programme based on the World Health Organization Health Promoting Schools Model among children attending schools officially designated as urban and disadvantaged. We present here the first results on physical and emotional health and the relationship between childhood depression and demographic and socioeconomic factors. METHODS: The Healthy Schools Programme evaluation was a 3-year longitudinal outcome study among urban disadvantaged children aged 4 to 12 years. Physical and psychological health outcomes were measured using validated, international instruments at baseline. Outcomes at baseline were compared with international norms and where differences were found, results were statistically modeled to determine factors predicting poor outcomes. RESULTS: A total of 552 children responded at baseline, representing over 50% of all eligible children available to participate from 7 schools. Findings at baseline revealed that in general, children did not differ significantly from international norms. However, detailed analysis of the childhood depression scores revealed that in order of importance, psychological well-being, the school environment, social support, and peer relations and age were statistically significant predictors of increased childhood depression in children under 12 years of age. CONCLUSION: Future health and well-being studies in schools among urban disadvantaged children need to broaden their scope to include measures of depression in children under 12 years of age and be cognisant of the impact of the school environment on the mental and emotional health of the very young.