In mouse and most other mammalian species, the paternal and maternal genomes undergo parent-specific epigenetic reprogramming during preimplantation development. The paternal genome is actively demethylated within a few hours after fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg chromatin for somatic development. Disturbances in this highly coordinated process may contribute to developmental failures and defects in mammals. The frequency and severity of abnormal phenotypes increase after interfering with or bypassing essential steps of gametogenesis, early embryogenesis, or both. Nevertheless, it is plausible that normal fertilization, assisted reproduction, and embryo cloning are all susceptible to similar dysregulation of epigenetic components. Although the mouse maybe an excellent model for early human development, species and strain differences in the molecular and cellular events shortly after fertilization may have important implications for the efficiency of epigenetic reprogramming and the incidence of reprogramming defects. Some species, i.e., rabbit and sheep, do not require drastic genome-wide demethylation for early development, most likely because the transition from maternal to embryonic control occurs relatively late during preimplantation development. A better understanding of key reprogramming factors--in particular the demethylase activity in the fertilized egg--is crucial for improving human infertility treatment and the efficiency of mammalian embryo cloning.