The aim of the present was to assess the association between MIH and tooth agenesis (TA) in orthodontic patients from the Federal University of Rio Grande do Norte, Natal, Brazil. A cross-sectional study was performed to evaluate the presence of MIH and TA in a sample of 371 pretreatment orthodontic records from patients aged 9-18years. Statistical analyses were performed using the Chi-square and Fisher's exact tests, and logistic regressions. There was a statistically significant association between the prevalence of tooth agenesis and MIH. A higher percentage of third molar agenesis, maxillary premolar agenesis, and mandibular second premolar agenesis was observed among children with MIH-affected teeth. Patients with MIH had a 2.43 times greater chance of third molar agenesis, and a 5.88 times higher likelihood of mandibular premolar agenesis. There is a weak association between MIH and TA. Furthermore, the presence of hypomineralised molars increases the risk of tooth agenesis.