Aim This was to study the prevalence of molar incisor hypomineralisation (MIH) among school children residing in a fluorosis endemic area in Tamilnadu (Salem, India). Methods A target sample of 5000 children of age ranging between 9 and 14 years, comprising 250 children from each of 20 blocks of Salem, participated in this study. The examination was completed in their respective schools by a calibrated examiner using EAPD criteria. Results Of 4989 children examined, 384 children had MIH. A prevalence of 7.3 %. The MIH found in girls was 8.9 % compared with 6.1 % in boys. Single-tooth involvement of MIH was seen predominantly in incisors (2.24 %), whereas with molars usually three teeth were involved (1.1 %). MIH with caries involvement was found in 51 % of the teeth. Conclusion The prevalence of MIH in the endemic fluorosis district was found to be 7.3 %. A gradual increase in MIH was seen with age due to post enamel breakdown. Caries involvement was also seen in more than 50 % of the MIH-involved teeth. This prevalence study for molar incisor hypomineralisation (MIH) is rare in the literature, especially in a fluorosis endemic district in Tamilnadu.