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At least in Fallout 3, yes it does. It will cause regulators, which are basicly vigilantes of the wasteland, to come after you to kill you, prevent you from getting Fawkes, Butch, Sergeant RL-3, or Star Paladin Cross from following you, and will negatively affect your interactions with certain characters in some situations. However, having bad karma also has good consequences. It will allow you to recruit Clover and Jericho, and will positively affect your interactions with certain characters in some situations.