Flies are small flying insects that appeared in The Binding of Isaac series. They may refer to:
- Black Fly - A very common black-colored fly enemy.
- Attack Fly - A red/black flashing fly enemy.
- Moter - A pair of Attack Flies joined together.
- Eternal Fly - A pure white-colored fly enemy added to the Wrath of the Lamb DLC.
- Pooter - A bloated version of normal flies.
- Fat Fly - A fatter and stronger version of the Pooter added to the Wrath of the Lamb DLC.
- Boom Fly - A larger version of normal flies that can explode upon death.
- Red Boom Fly - A red-colored Boom Fly.
- Drowned Boom Fly - A blue-colored Boom Fly added to the Afterbirth DLC for Rebirth.
- Sucker - More powerful version of normal flies.
- Spit - A green-colored Sucker.
- Swarm Fly - A yellow-colored fly added to the Afterbirth DLC for Rebirth.
- Dart Fly - A type of fly looking similar to that of the Swarm Fly added to the Afterbirth DLC for Rebirth.
- Ring Fly - A pink-colored fly in Rebirth.
- Level 2 Fly - A much stronger variant of normal flies in Rebirth.
- Full Fly - A powerful version of normal flies related to Level 2 Flies in Rebirth.
- Hush Fly - A bluer-colored fly added to the Afterbirth DLC for Rebirth.
- Ball of Flies - A double Moters fused together added to the Eternal Edition for the original game only.
- The Duke of Flies - The boss of the Basement and Cellar.
- The Husk - A posthumous counterpart of The Duke of Flies added to the Wrath of the Lamb DLC.
- Forever Alone - A fly familiar item that orbits around Isaac.
- Papa Fly - A blue fly item added to the Afterbirth DLC in Rebirth.
- Pretty Fly - A collectible passive item.
- Beelzebub - The transformation in Rebirth based on the demon of the same name being titled as "lord of the flies".