Background: Annually, around 7.9 million children are born with birth defects and the contribution of congenital malformations to neonatal mortality is generally high. Congenital malformations in children born to mothers with hypertensive disorders during pregnancy has marginally been explored. Methods: Country incidence of congenital malformations was estimated using data on the 310 401 livebirths of the WHO Multicountry Survey which reported information from 359 facilities across 29 countries. A random-effect logistic regression model was utilized to explore the associations between six broad categories of congenital malformations and the four maternal hypertensive disorders "Chronic Hypertension", "Preeclampsia" and "Eclampsia" and "Chronic hypertension with superimposed preeclampsia". Results: The occupied territories of Palestine presented the highest rates in all groups of malformation except for the "Lip/Cleft/Palate" category. Newborns of women with chronic maternal hypertension were associated with a 3.7 (95 % CI 1.3-10.7), 3.9 (95 % CI 1.7-9.0) and 4.2 (95 % CI 1.5-11.6) times increase in odds of renal, limb and lip/cleft/palate malformations respectively. Chronic hypertension with superimposed preeclampsia was associated with a 4.3 (95 % CI 1.3-14.4), 8.7 (95 % CI 2.5-30.2), 7.1 (95 % CI 2.1-23.5) and 8.2 (95 % CI 2.0-34.3) times increase in odds of neural tube/central nervous system, renal, limb and Lip/Cleft/Palate malformations. Conclusions: This study shows that chronic hypertension in the maternal period exposes newborns to a significant risk of developing renal, limb and lip/cleft/palate congenital malformations, and the risk is further exacerbate by superimposing eclampsia. Additional research is needed to identify shared pathways of maternal hypertensive disorders and congenital malformations.