This paper addresses the possibilities of germplasm contamination by viral, bacterial and parasitic agents and the risk of their transmission by assisted reproductive technologies (ART). The potential for germplasm contamination with infectious pathogens during the collection, in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), embryo cloning by nuclear transfer and embryo culture is discussed. Special attention is also given to the sanitary aspect of cryopreservation and long term cryobanking of germplasm. The experimental data show that many human and animal pathogens can be associated with semen and embryos, but only a few have the ability to enter the sperm or penetrate the intact zona pellucida and replicate in embryonic cells. There is always a possibility of viral or bacterial agents being in contact with oocytes within the ovary or ovarian follicular fluid before fertilization, or later, through agents being introduced inadvertently into the IVF system. As with in vivo produced embryos, there is no one procedure that is fully effective in rendering IVF embryos free of all microorganisms. At present, sperm and embryo washing are the most effective procedures in reducing the number of microorganisms associated with germplasm and as preventive measures of disease transmission through ART. It has been concluded that the risk of disease transmission by new reproductive technologies can be minimized when sanitary protocols, recommended for animal embryo processing by the International Embryo Transfer Society, are applied.