In the late 1970s, embryo pathogen research was spawned. Initially, a great deal of funding was available to groups involved in embryo pathogen research. However, following years of research, and development of competent embryo processing procedures endorsed by the International Embryo Transfer Society (IETS), a growing belief developed that embryo transfer (ET) is innately safe and so funding for embryo pathogen research has since dwindled portentously. Even with continued growth of the ET industry and specifically with tremendous changes involving in vitro technologies, and recent outbreaks involving pathogens of concern, funding of ET research has not been a priority and/or a focus area for funding agencies for the last number of years. Funding issues are not the only challenge in embryo pathogen research but it is the primary challenge since no amount of research can be pursed without funding. Some of these additional challenges include; a large number and variety of pathogens which need to be systematically investigated including new and reemerging pathogens, utilization of animal origin products which have the potential to harbor and transmit pathogens, the ability of pathogens to adapt and change to their hosts and environment resulting in variation of affinity and virulence, reliable testing of these pathogens and trained personnel to perform studies, collect and interpret data and to knowledgeably handle pathogens that have zoonotic pathogens. This paper reviews these challenges facing embryo pathogen research today