Amniotic fluid abnormalities may be associated with adverse perinatal outcomes, some of which are endocrine related. To evaluate whether in utero exposure to amniotic fluid abnormalities is associated with long-term endocrine morbidity in the offspring. In this cohort study, the incidence of long-term endocrine disorders was compared between singletons exposed and non-exposed to oligohydramnios or polyhydramnios. 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 test p < 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. In utero exposure to isolated amniotic fluid abnormalities is independently associated with long-term endocrine morbidity in the offspring.