Introduction: Hyperthyroidism in pregnancy is a serious condition and its management is complex. Whilst carbimazole/methimazole (CBZ/MMI) and propylthiouracil (PTU) have similar efficacies in controlling hyperthyroidism, their risk of side effects such as major congenital abnormalities and hepatotoxicity are different. Methods: Various combinations of the terms ‘anti-thyroid drugs’, ‘thionamide’, ‘carbimazole’, ‘methimazole’, ‘propylthiouracil’, ‘pregnancy’, ‘side effects’, ‘agranulocytosis’, ‘birth defects’, ‘congenital malformations’, ‘embryopathy’, ‘aplasia cutis’, ‘hepatotoxicity’, ‘hepatic failure’, ‘maternal’ and ‘fetus’ were used to search MEDLINE and the Cochrane library. The references of retrieved papers were also reviewed. Results: There is increasing evidence for a CBZ/MMI embryopathy, whilst data remain lacking for major congenital abnormalities with PTU. In contrast, PTU is associated with increased risk of severe liver injury. Management strategies to reduce these risks by using PTU in the first trimester and CBZ/MMI in the later trimesters remain untested. Conclusion: More evidence is still needed in defining the relative risks between CBZ/MMI and PTU of major congenital abnormalities and severe liver injury in pregnancy. Studies are also needed to establish the suitability of recent management suggestions in switching from PTU to CBZ/MMI after the first trimester. Major adverse outcomes secondary to CBZ/MMI and PTU are rare, and inadequately treated hyperthyroidism poses a far greater risk.