At least in 2006-2007 it was 97% of companion animals, and we only know this because the courts asked for these internal documents:

Death toll up to 17,400; overdue report describes PETA's deadliest year ever

WASHINGTON, Jan. 10 /PRNewswire-USNewswire/ -- An official report from People for The Ethical Treatment of Animals (PETA), submitted nine months after a Virginia government agency's deadline, shows that the animal rights group put to death more than 97 percent of the dogs, cats, and other pets it took in for adoption in 2006. During that year, the well-known animal rights group managed to find adoptive homes for just 12 pets. The nonprofit Center for Consumer Freedom (CCF) is calling on PETA to either end its hypocritical angel-of-death program, or stop its senseless condemnation of Americans who believe it's perfectly ethical to use animals for food, clothing, and critical medical research.

Not counting animals PETA held only temporarily in its spay-neuter program, the organization took in 3,061 "companion animals" in 2006, of which it killed 2,981. According to Virginia's Department of Agriculture and Consumer Services (VDACS), the average euthanasia rate for humane societies in the state was just 34.7 percent in 2006. PETA killed 97.4 percent of the animals it took in. The organization filed its 2006 report this month, nine months after the VDACS deadline of March 31, 2007.

That also does not include the animals that PETA handed off to other shelters which may have also been euthanized.