This article reviews the risks of childhood malignancies and imprinting disorders in children born after assisted reproductive technology (ART). It is recognized that there is a theoretical potential of developing an excess of malignancies in children born after ART. With the advancement and introduction of newer techniques in ART there is an increase in the micromanipulation of gametes and embryos in vitro and extended exposure to the in vitro environment. These include the use of gonadotropins for superovulation, intracytoplasmic sperm injection, blastocyst culture, assisted hatching, and preimplantation genetic diagnosis. Although these approaches aim to enhance pregnancy rates and its outcome, the risk of associated long-term health hazards cannot be disregarded. More recently there is some evidence suggesting a link between ART and epigenetic alterations leading to DNA modifications and imprinting disorders. Two of these genetic imprinting disorders that are known to cause birth defects and childhood malignancies, Beckwith-Wiedmann syndrome and Angelman syndrome have been associated with ART. Systemic reviews of the literature identified published studies, but were unable to identify the precise risks of imprinting disorders and childhood cancers in children conceived with ART. Overall, most studies have not shown any increase in the incidence of childhood cancers after ART. With more women resorting to ART, careful counseling should be offered to all couples especially those requiring intracytoplasmic sperm injection for abnormal sperm parameters.