Background Amniotic fluid abnormalities may be associated with adverse perinatal outcomes, some of which are endocrine related. Objective To evaluate whether in utero exposure to amniotic fluid abnormalities is associated with long-term endocrine morbidity in the offspring. Study design In this cohort study, the incidence of long-term endocrine disorders was compared between singletons exposed and non-exposed to oligohydramnios or polyhydramnios. Results During the study period, 195 943 newborns were included in the study, of them 2.0% (n = 4072) and 2.9% (n = 5684) were exposed to oligohydramnios and polyhydramnios, respectively. Long-term endocrine morbidity was higher among children exposed to isolated amniotic fluid disorders, as was also noted in the Kaplan-Meier survival curve (log-rank testp < 0.001). Abnormal amniotic fluid volume was found to be independently associated with long-term endocrine morbidity of the offspring according to a Cox regression model controlled for clinically related confounders. Conclusion In utero exposure to isolated amniotic fluid abnormalities is independently associated with long-term endocrine morbidity in the offspring.