Scabies and impetigo are common and important skin conditions which are often neglected in developing countries. Limited data have been published on the prevalence of scabies and impetigo in Timor-Leste. Sequelae including cellulitis, bacteraemia, nephritis, acute rheumatic fever and rheumatic heart disease contribute significantly to the burden of disease.School students were recruited from schools in Dili (urban) and Ermera (rural) in Timor-Leste for an epidemiological study in October 2016. A standard questionnaire was used to record demographics, anthropometry and skin examination results. Impetigo and scabies were diagnosed based on clinical examination of exposed surfaces, and clinical photographs were reviewed for correlation by an infectious diseases paediatrician. Prevalence of scabies and impetigo were calculated and binary risk factor associations were described using relative risks and 95% confidence intervals. Adjusted odds ratios were calculated using logistic regression multivariate analysis. Continuous variables were analysed for associations using the Mann-Whitney Rank Sum test.The study enrolled 1396 students; median age 11 years (interquartile range (IQR) 9-15). The prevalence of scabies was 22.4% (95% CI 20.2-24.7%) and active impetigo 9.7% (95% CI 8.3-11.4%); 68.2% of students had evidence of either active or healed impetigo. Students in Ermera were more likely than those in Dili to have scabies (prevalence 32.0% vs 5.2%, aOR 8.1 (95% CI 5.2-12.4), p<0.01). There was no difference in the prevalence of active impetigo between urban and rural sites. More than a third of participants were moderately or severely underweight. Stunting was markedly more common in the rural district of Ermera.Scabies and impetigo are common in Timor-Leste, with very high prevalence of scabies in the rural district of Ermera. Improvements in prevention and treatment are needed, with prioritised activities in the rural areas where prevalence is highest.