The new EU rules will become effective in April 2010, requiring that either slaughtered animals have complete health records showing they have not received banned substances or a 180-day quarantine for the horses.
Equine welfare advocates have warned about contamination of American horse meat for years.
Substances banned from food animals range from toxic wormers to phenylbutazone (PBZ), the "aspirin" of the horse world, and even include fertility drugs that can cause miscarriages in women.
"PBZ is a known carcinogen and can cause aplastic anemia (bone marrow suppression) in humans," says Equine Welfare Alliance (EWA) member, Dr Ann Marini, Ph.D., M.D.
But the list of contaminants is not limited to conventional drugs.
"Some of the garbage 'treatments' that are given to performance horses included iodine-peanut oil injections along the spine, anabolic steroids, cocaine, amphetamines, opioids and even snake venom," explains Dr Nicholas Dodman, a veterinarian at Tufts University.
The new rules will mean that horses coming from auctions and other sources in the United States will have to be kept drug-free on a feedlot for half a year.
Producers estimate that feeding horses that long will more than double their cost, making them less competitive with horses from other sources. And that is likely to be only half their problem.
Equine Welfare Alliance member Christy Sheidy, of Another Chance 4 Horses, routinely rescues slaughter-bound horses from Pennsylvania's New Holland auction.
"Outbreaks of diseases like strangles and shipping fever will be inevitable in these quarantine feedlots," warns Sheidy. "Left untreated, many horses may die before they can be slaughtered."
Treating the horses would restart their quarantine time.
In recent years, European authorities have cracked down on horse-meat producers within the EU, requiring a "passport" system that specifically documents whether a horse has received such substances. Owners must state whether their horses are intended for slaughter.
US Department of Agriculture statistics show that in 2008, the US exported 56,731 horses to Mexico and 77,073 horses to Canada for slaughter, resulting in the second-highest slaughter total since 1995.
Diners abroad have no idea whatsoever what dangerous chemicals they are eating in the American horsemeat that is shipped from plants across US borders.
In an interview with the alliance, Henry Skjerven, a former director of the Natural Valley Farms slaughter operation in Saskatchewan, Canada, said: "Unfortunately, North America, US and Canada, were never geared for raising horses for food consumption. The system as it stood when we were killing horses was in no way, shape or form, safe, in my opinion."
Skjerven went on to say: "We did not know where those horses were coming from, what might be in them or what they were treated with.
"I was always in fear - I think that it was very valid - that we were going to send something across there [to the EU] and we were simply going to get our doors locked after we had some kind of issue with the product."
Skjerven's plant began killing horses in September of 2007 for Belgium's Velda Group following the closing of their Cavel slaughter plant in DeKalb, Illinois.
Natural Valley's horse slaughter plant was closed by the Canadian Food Inspection Agency in January of 2009, for health issues.
Unlike Canada, horses going to Mexico are killed in two types of slaughter plants. The three largest plants export the meat to the EU and will fall under the same new rules.
Mexican authorities have yet to announce whether their smaller plants, that provide meat for domestic consumption, will be required to follow the new rules.
"We don't need to eat horses. Horses are for riding, jumping and doing a whole lot of great things. They're not food," concluded Skjerven.