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Ears are found on good characters (such as members of the Brotherhood of Steel or Regulators) when the PC has the Contract Killer perk. Daniel Littlehorn from Littlehorn & Associates, located at the Scrapyard, rewards you with 15 caps and bad karma for each ear, this is the bad Karma alternative to the Lawbringer perk(with Fingers instead of ears).
While you cannot kill essential characters, an ear will spawn in their inventory each time they are knocked unconscious. These can then be pick-pocketed from them, yielding an unending source of ears. How a person has an unlimited supply of ears remains a mystery.
If the player has bad karma he wil occasionally encounter a regulator hitsquad. These will yield 3 ears which can then be sold for 45 caps and bad karma , even if you go up to neutral or good karma they will still be after you so you can make some pretty decent caps out of them,if you have enough patience.
Trivia
The item itself may be a reference to the Vietnam War, where American troops would often sever the ears of Vietnamese soldiers as a post-death act of spite (the Vietnamese religion dictated that a man's spirit could only go to the afterlife if his body was whole).
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