Objective: To determine the prevalence of molar-incisor hypomineralization (MIH) in the permanent dentition and assess the factors associated with these change in schoolchildren of São Luís, Brazil. Material and Methods: Overall, 1179 students aged 7-14 years of both sexes were included, all with permanent first molars and incisors erupted in the oral cavity. Oral clinical examination to assess the prevalence of HMI was held at school, under natural light. In the second stage, to assess factors associated with HMI, a case-control study was conducted, in which cases were children diagnosed with HMI (n = 14) and as controls, the schoolchild's brother (family control, n = 10 ) and another schoolchild in the same age group born in the same locality (community control, n = 14). A semistructured questionnaire was completed by mothers to identify possible factors associated with HMI, such as maternal education, family income, data from pregnancy and child's medical history in the first three years of life. Logistic regression analysis was used to estimate odds ratios (Odds Ratio -OR) and their confidence intervals at 95% (CI 95%) to assess crude and adjusted associations for confounders. Results: A prevalence of 2.5% of HMI was estimated. No association was found for the etiologic factors surveyed. Conclusion: The prevalence of HMI was lower than that reported in other cities in Brazil, but similar to data from other countries. At the difficulty and complexity in establishing the etiologic factors of HMI, cohort studies are required to clarify this change.