Background: Molar–Incisor Hypomineralization (MIH) represents a developmental enamel defect of systemic origin, typically affecting the first permanent molars and often the incisors. Within the limitations of this study, several associations were observed between perinatal factors and MIH-related outcomes. However, most of these connections were not retained in adjusted analyses. Febrile illness during the first year of life showed a significant association with hypersensitivity. Methods: A structured 30-item questionnaire was distributed to mothers of 50 children diagnosed with MIH between February and March 2024. Data was analyzed using chi-square tests, with p < 0.05 considered significant, and univariate and multivariate logistic regressions at 95% confidence interval. Clinical diagnosis followed the Weerheijm (EAPD) criteria. Results: Maternal medication during pregnancy (antibiotics, antiepileptics, asthma drugs) was significantly associated with preterm birth (p = 0.01). Low birth weight correlated with tooth eruption disorders (p = 0.009) and perinatal complications such as hypoxia and respiratory distress (p = 0.0001). Fluoride application demonstrated a protective effect against discolorations (p = 0.005), caries (p = 0.002), and hypersensitivity (p = 0.01). In the multivariate model, febrile illness during the first year of life may be associated with hypersensitivity in MIH-affected teeth (aOR = 5.71, 95% CI: 1.01–32.27, p = 0.049). Conclusions: Maternal medication and perinatal complications, particularly low birth weight, were associated with MIH occurrence. Preventive strategies emphasizing maternal health, early screening, and remineralization-based therapies can mitigate long-term oral health impacts.