Objective: To evaluate maternal and fetal factors associated with congenital malformations in patients with polyhydramnios. Study Design: The study group consisted of 275 singleton pregnancies with an amniotic fluid index (AFI) >25.0 cm. An equal number of controls were matched for maternal age, gravidity, parity and gestational age. The proportion of cases and controls with malformations was compared. Polyhydramnios cases were categorized into three groups by severity: mild (AFI 25–30 cm), moderate (AFI: 30.1–35.0 cm) and severe (AFI >35.1 cm). Among cases, logistic regression analysis was utilized to estimate the risk for fetal congenital malformations in relation to severity of polyhydramnios, estimated fetal weight, maternal diabetic status and gestational age at delivery. Results: Congenital malformations were detected in 40 of 275 cases (14.5%) with polyhydramnios and in 9 cases (3.3%) of the control group (p < 0.01). The relative risks of congenital malformations increased with the severity of polyhydramnios: 3.2 (95% CI 1.5–6.8), 5.7 (95% CI 2.4–13.3) and 13.1 (95% CI 5.8–29.5) for mild, moderate and severe polyhydramnios, respectively. Congenital malformations among polyhydramnios cases were present in 54.5% of small-for-gestational age fetuses, in contrast to 12.7% for average-for-gestational age fetuses and 10.8% for large-for-gestational age fetuses (p < 0.001). Maternal diabetic status did not significantly affect the fetal anomaly rate once polyhydramnios was detected. Premature newborns in the polyhydramnios group had a higher malformation rate (24%) than did term newborns (11.3%) (p < 0.02). In the study group, multiple logistic analysis confirmed the significance of severe polyhydramnios, small-for-gestational age status and preterm delivery as independent contributors to the malformation risk. Conclusions: Polyhydramnios (AFI >35 cm), small-for-gestational age fetus and preterm delivery are independent risk factors for congenital malformations.