The objective of our study was to evaluate the association of molar-incisor hypomineralizations (MIHs) with prospectively collected potential causative factors from the first 4 years of life, e.g. respiratory diseases, breastfeeding, maternal smoking and parental education. A total of 692 children (10 years old) from the GINI birth cohort study participated. The dental examination included the registration of enamel hypomineralizations (EHs) according to the EAPD criteria. Children with EH were sub-categorized into those with at least one EH (MIH/1), those with a minimum of one EH on at least one first permanent molar (MIH/2) and those with EH on at least one first permanent molar and a permanent incisor (MIH/3). All relationships between causative factors and caries or MIH were evaluated using simple and multiple logistic regression analyses. EHs were observed in 37.9% (MIH/1), 14.7% (MIH/2) and 9.2% (MIH/3) of all subjects. After adjustment for confounding factors, 10-year-old children with at least one episode of respiratory disease had a significantly higher risk (2.48 times, adjusted OR) for the development of MIH/3. In case of breastfeeding, a non-significant association was observed. None of the tested factors was associated with either MIH/1 or MIH/2. Early respiratory diseases seem to be directly or indirectly related to MIH/3 only. The role of (systemic) medications used for treatment of these diseases needs to be investigated in future studies.