- Objective To evaluate whether offspring of women with müllerian anomalies are at an increased risk for long-term pediatric morbidity. Study design A population-based cohort study compared the incidence of long-term (up to the age of 18 years for offspring) hospitalizations due to cardiovascular, endocrine, neurological, hematological, respiratory and urinary morbidity of offspring to mothers diagnosed with uterine anomalies. Deliveries occurred between the years 1991 and 2013 in a tertiary medical center. Multiple pregnancies, unknown gestational age, gestational age of less than 24 weeks, perinatal mortality, and fetuses with congenital malformations were excluded. Kaplan–Meier survival curves were used to compare cumulative morbidity incidence. Survival analysis for clustered data was performed for each major-system pediatric hospitalization. Results During the study period 253,808 deliveries met the inclusion criteria; 0.48% (n = 1230) of which occurred in women diagnosed with müllerian anomalies. In the Kaplan–Meier survival curve, children born to mothers with müllerian anomalies did not have a significantly different cumulative incidence of any of the long-term pediatric morbidities, compared with the comparison group. In the multivariable survival analysis for clustered data, after adjustment of maternal clusters, maternal age, gestational age and birthweight, müllerian anomalies did not exhibit an independent association with long-term morbidities of the offspring. Conclusion Müllerian anomalies do not appear to have an independent impact on long-term morbidity of the offspring.