EIA is transmitted by the exchange of certain bodily fluids, usually blood, from an infected to a noninfected animal. One mode of transmission is through insect bites. Horseflies, stable flies, and deer flies are blood feeders. Their bites are painful, and an animal often interrupts the insects' feeding, forcing them to relocate. A fly usually will have residual blood on its mouth parts from an interrupted meal. If the fly moves from an infected to a noninfected animal, the virus may be introduced into the noninfected animal when the insect breaks the skin.

The virus is also transmitted by mechanical means. Instruments, such as hoof knives, needles (tattooing or bleeding), syringes, etc., that were previously used and contaminated with blood from an infected animal are mechanical procedures of infecting a healthy animal. Blood transfusions have also been implicated in transmitting the virus.

During gestation, if the levels of virus in the blood are high enough, transplacental infection of the foal is possible. Approximately 10 percent of foals delivered from infected mares are infected at birth and remain life-long carriers of the virus. Because of the presence of maternal antibodies to the virus in the mare's colostrum, foals born to infected mares will themselves be antibody positive at 24 hours of age. Maternally acquired passive antibodies should be gone by six months of age. If the foal is infected at birth, its own antibodies will persist after six months.