The aim of the present review is to provide information to researchers and practitioners concerning the reasons for the altered viability and the medium- and long-term consequences of cryopreservation of manipulated mammalian embryos. Embryo manipulation is defined herein as the act or process of manipulating mammalian embryos, including superovulation, AI, IVM, IVF, in vitro culture, intracytoplasmic sperm injection, embryo biopsy or splitting, somatic cell nuclear transfer cloning, the production of sexed embryos (by sperm sexing), embryo cryopreservation, embryo transfer or the creation of genetically modified (transgenic) embryos. With advances in manipulation technologies, the application of embryo manipulation will become more frequent; the proper prevention and management of the resulting alterations will be crucial in establishing an economically viable animal breeding technology.