Embryonic mortality (EM) has a substantial impact on the fertility of domestic animals. Most of the embryonic losses occur during the first days after fertilization and during the process of implantation. Causes of EM can be divided into infectious and non-infectious categories. Primary attention has often been given to infectious agents but non-infectious causes probably account for 70% or more of the cases of embryonic death. Infection of the embryonic environment can be caused by specific and non-specific uterine pathogens. Specific uterine infections are caused by a number of viruses, bacteria and protozoa that enter the uterus by the haematogenous route or via the vagina. Non-specific pathogens are mainly bacteria that enter the uterus by ascending infection. Uterine pathogens may cause EM by changing the uterine environment (endometritis) or by a direct cytolytic effect on the embryo. Non-infectious causes of EM such as chromosomal aberrations, external factors (e.g., high ambient temperature and nutritional factors) and maternal factors (e.g., hormonal imbalances and age) are multifactorial and difficult to diagnose.