Background: Inequalities in oral health disproportionately affect low and middle income countries and a pattern of increased prevalence of dental caries in children has been reported. Objectives: To determine the burden of disease and behavioural and toothache history of six- and 12-year-old Malawi schoolchildren. Methods: Ethical approval was granted by Malawi’s National Health Sciences Research Committee. The survey was undertaken by nine Malawian dental therapists and three UK dentists in 24 schools. Stratified cluster sampling ensured that the children were representative of Malawi’s three Regions. Dental caries (into dentine), fluorosis, oral hygiene and PUFA index data were collected via a dental examination. Questionnaires were completed by each child and by the Head Teacher from each school. Results: A total of 1,330 six-year-old and 1,611 12-year-old children were examined, evenly split between the sexes. Dental caries was identified in 47% of six-year-olds and 23% of 12-year-olds. None of the children had filled teeth. The mean dmft/DMFT for children with caries experience was 3.0 for six-year-olds and 1.8 for 12-year-olds. Dental fluorosis was recorded for 7% of 12-year-olds. A history of toothache was reported by 29% of six-year-olds and 42% of 12-year-olds. Conclusions: The prevalence of caries and absence of signs of past clinical care highlight the need to implement activities identified in Malawi’s National Oral Health Policy around the provision of appropriate preventive and treatment services for children.