Gestational trophoblastic disease (GTD) is a heterogeneous group of neoplastic conditions which arise from abnormal proliferation of trophoblastic tissues during pregnancy. The proper differentiation and function of trophoblast during embryo implantation and placentation is essential for successful pregnancy. Epigenetic mechanisms, which provide transcriptional control of gene expression without alterations in gene sequence, are critical components of normal development of placenta and embryo. Genomic imprinting is an epigenetic form of gene regulation which results in the parent-of-origin specific gene expression and leads to functional non-equivalency of parental genomes. This indicates that the presence of both the maternal and paternal genomes is required in the zygote for normal development. Genomically imprinted genes regulate embryonic and placental development and have major functions at the feto-maternal interface, including nutrient transport, trophoblast proliferation, invasion and angiogenesis. Abnormalities in genomic imprinting, including altered ratio between maternal and paternal genomes, lead to numerous disorders of fetal and placental growth, and have a key role in the pathogenesis of GTD. The constant progress in the field of reproductive (epi)genetics indicates that modification of epigenetic mechanisms which control gene expression will have an important role in the diagnosis, prognostic assessment and treatment of pathological pregnancies. In this review we present the current understanding of the (epi)genetic mechanisms involved in the etiology of GTD.