BACKGROUND In China, there is a large migrant population. A significant proportion of children of the migrant population in China are not able to attend public schools due to the lack of local household registration (HuKou). They turn to privately-operated migrant schools, which are usually under-funded, have bad environmental facilities and are inadequately staffed compared to public schools. This study aims to describe the dental caries status of students from migrant primary schools in Shanghai Pudong New Area and factors that influence their caries status. METHODS Children (7-12 years old) from migrant primary schools in Shanghai Pudong New Area were randomly selected through a multi-stage cluster sampling method. Following the recommendation of the World Health Organization, caries experiences were recorded using the dmft index. A questionnaire to survey the children's socio-demographic characteristics and oral health-related behaviours was completed by the children's parents or guardians. RESULTS A total of 1385 children in migrant primary schools were invited, of which 1323 joined the survey (95.5 %). Among all the surveyed subjects, the prevalence rate of dental caries was 74.7 % (65.7 % for primary teeth and 28.1 % for permanent teeth). The mean (SD) dmft scores were 3.17 (3.12), 2.74 (3.02) for the primary teeth and 0.44 (0.84) for the permanent teeth, and 99.5 % of the carious teeth received no treatment. CONCLUSIONS Students from migrant primary schools in Shanghai Pudong New Area had bad conditions of dental caries and most of the carious teeth were left untreated. The caries experience was associated with tooth brushing habits, snacking habits, dental visit and gender.