PETA was criticized in 2005 when police discovered at least 80 animals had been left in dumpsters over the course of a month by two PETA employees. The employees approached the dumpster in a van registered to PETA and left behind 18 dead animals. Thirteen more were found inside the van. The animals had been killed by PETA employees after being taken by PETA from shelters in Northampton and Bertie counties.[82] Officials from both counties said they were under the impression that the animals would be euthanized only if a home could not be found for them, and after being fully evaluated by a veterinarian. Both counties suspended their agreements with PETA after the incident.

Among the bodies in the dumpster were a cat and two of her kittens, given to PETA by veterinarian Patrick Proctor of Ahoskie Animal Hospital. According to Proctor, the two kittens were very adoptable, and he said the PETA employees claimed they would have no trouble finding homes for them. In an interview with CNN, Ingrid Newkirk said that Proctor — who himself carries out euthanasia on behalf of PETA — was not present when the kittens were removed and was therefore not in a position to know what PETA's employees had said. Newkirk added that it was unlikely the employees said they could find homes for the animals, given that the veterinarian's assistant handed the animals to PETA precisely because she knew homes could not be found. “If the veterinarian couldn't find homes for a few kittens and a cat, which is surprising, if they have clients coming in, then that's why they called us, because they know we don't have a magic wand either,” Newkirk told CNN.

PETA condemned the dumping as against their policy, and suspended one of the employees involved for 90 days. Police charged the two employees with 31 felony counts of animal cruelty and eight misdemeanor counts of illegal disposal of dead animals. In October, these charges were dropped, and replaced with 42 combined counts of animal cruelty, and 3 counts of “obtaining property under false pretense”. A trial date was set for August 16, 2006.

According to the Wally Swett, President of Primarily Primates, PETA killed 1,946 pets in its home state of Virginia in 2005, transferring or adopting out 215, and killed 141 wild animals in the same year, transferring or releasing 52. In 2004, PETA killed 2278 animals while finding homes for 368 animals. Columnist Debra J. Saunders of the San Francisco Chronicle, quoting the Center for Consumer Freedom (CCF) data based on PETA's filing with the state of Virginia, has said that PETA killed over 10,000 animals from 1998 to 2003.