The aim of the present paper was to review some features related to the risk analysis of three types of embryos to be transferred, namely the in vivo derived, the in vitro produced and the cloned ones. For in vivo-collected embryos, a considerable number of experiments and scientific investigations have been performed and hundreds of thousands of embryos are transferred annually with no contamination of associated diseases. Provided that the code of practice such as that published by the International Embryo Transfer Society is strictly followed by the embryo transfer practitioners, the statement made some 17 years ago saying that the in vivo-derived embryo transfer was the safest way of exchanging genes remains entirely true, thanks to the professionalism of the embryo transfer industry. For the in vitro-produced embryos, some particular rules have to be followed because of specific risks for some pathogens to strongly adhere to the zona pellucida of such embryos. There are some means to monitor and control those effects, and the transfer of in vitro-produced embryos can also be a very safe way to exchange genes around the world. The third type of embryos, the cloned ones, is a quite different category and the risk analysis to be soundly made still needs a lot of investigations so as to characterize the potential risks if there are, in terms not only of disease transmission but also in terms of public health, zoonotic risks as well as those related to quality and safety of food. The problem in this regard, is more directly addressed for offspring of clones than to the cloned embryos themselves. Published data on this issue are increasing in numbers so that progress in that area is expected in the few years to come.