Disinfection of waste can be carried out by first cutting the waste into small pieces to expose surfaces in the waste and then simultaneously spraying the waste pieces with disinfectant and agitating them. The waste pieces are agitated by applying sufficient vacuum to suck the waste pieces through a processing system, the vacuum creating a wind inside the system that sweeps up the waste pieces, suspends them in air, and keeps them separate from one another, thereby exposing substantially all surfaces of the waste pieces to the sprayed disinfectant.