OBJECTIVE To compare 2-year cumulative survival rates in first permanent molars (FPM) with and without MIH and to investigate risk factors associated with caries incidence. METHODS A total of 142 children aged 5 to 6 years were recruited from all public schools in Botelhos, Minas Gerais, Brazil and 536 FPM were examined. A questionnaire was designed to collect sociodemographic background and behavioural information about children and their parents. Caries in FPM was recorded per surface in accordance with WHO methodology at baseline and once every 6 months over a period of two years. The survival analysis was conducted using the Weibull regression model with cure fraction. RESULTS MIH was present in 16.19% of children. The 2-year cumulative survival rates for FPM with and without MIH showed statistically significant differences, and visible plaque on anterior teeth had an effect on the survival rates. CONCLUSIONS Children with MIH and visible plaque on anterior teeth at baseline had a high risk for developing new caries lesions in their FPM over the course of two years. These variables should be considered in caries risk assessment in paediatric dental care.