BACKGROUND: Approximately half of women with intellectual and developmental disabilities (IDDs) lose custody of their children at some point in their child's development, but their rates of and risk factors for newborn discharge to child protective services from the birth hospitalization are relatively unknown. METHODS: We conducted a population-based study of newborns of 3845 women with IDDs and 379 834 women without IDDs in Ontario, Canada (2002-2012). We used modified Poisson regression to estimate adjusted relative risks (aRRs) and 95% confidence intervals (CIs) for discharge to child protective services directly from the birth hospitalization (1) comparing newborns of women with and without IDDs and (2) among newborns of women with IDDs according to sociodemographic, health, service, and perinatal characteristics. RESULTS: Approximately 5.7% of newborns of women with IDDs, compared with 0.2% of newborns of women without IDDs, were discharged to child protective services (aRR 8.10; 95% CI 6.51-10.09). Among newborns of women with IDDs, risk factors were maternal psychotic disorder (aRR 2.58; 95% CI 1.90-3.50), social assistance receipt (aRR 2.55; 95% CI 1.87-3.47), failure to receive an ultrasound by 20 weeks' gestation (aRR 1.76; 95% CI 1.32-2.34), and receipt of <4 prenatal visits by 36 weeks' gestation (aRR 1.71; 95% CI 1.05-2.78). CONCLUSIONS: Although women with IDDs are at risk for custody loss immediately postdelivery, certain subgroups are at higher risk than others. Women with vulnerabilities related to comorbid psychotic disorders, poverty, and inadequate prenatal care may benefit from tailored, behavior-based parenting interventions before and during pregnancy to prevent maternal-newborn separations.