Per NIH recommendation (Dec 2008), researchers that work with recombinant Drosophila should dispose of their euthanized flies either by autoclaving or disposing the flies in biohazardous waste containers for pickup by Environmental Health and Safety. Recombinant flies should never be disposed as regular trash unless they have been autoclaved.
Non-recombinant or wildtype flies are not regulated by NIH and can be disposed into the regular trash once they have been euthanized.
EHS can provide biohazardous waste containers upon request. When the containers are ready to be picked-up, the researcher should submit a Disposal Request Form (PDF) for biohazardous waste.