Objective: To determine the incidence of neurodevelopmental deviations and chronic diseases in children born after pregnancies initiated by ART. Study Design: Retrospective case-control study. Participants and Methods: The study included all children born at the Clinical Hospital Center Osijek from January 1, 2018, to December 31, 2020, from pregnancies following medically assisted reproduction, and each subsequent newborn conceived spontaneously listed in the medical documentation. Results: Pregnant women in the ART group were significantly older, more educated, more often in marital relationships, had significantly more comorbidities, and more frequently suffered from endocrinological and cardiovascular diseases. They had more complications during pregnancy, such as gestational diabetes, pregnancy hypertension, hypothyroidism, and anemia in pregnancy. There was a significantly higher number of multiple pregnancies, and pregnancies in the ART group were more often completed by emergency cesarean section, while vaginal delivery was more common in the control group. Mothers in the ART group more frequently maintained their pregnancies pharmacologically and used medication more often during pregnancy. Additionally, mothers in this group more often gave birth to preterm infants and infants with IUGR. Children in the ART group had significantly more frequent intracranial hemorrhages, longer stays in the intensive care unit, and more often had respiratory distress syndrome and needed mechanical ventilation. Speech development in children from the ART group was significantly slower, and these children more frequently attended neurodevelopmental rehabilitation. Conclusion: Pregnant women undergoing ART had more frequent comorbidities, were on polytherapy more often, and their pregnancies were more complicated with poorer outcomes and shorter gestation. Children conceived by ART had poorer perinatal outcomes and more frequently lagged in speech development.