It does not automatically or necessarily count against you, but there could be facts here that will hurt you in regards to custody, such as:1) If the girlfriend has a substance abuse problem or criminal record, or brings over friends/family with same; 2) If the girlfriend badmouths your wife or tries to undercut her with the children;3) If you and your girlfriend act inappropriately (excessive displays of intimacy, for example) around the children.4) If you have been inattentive to the children while your girlfriend is around.So it's behavior, not the fact that your girlfriend is there, which could be a custody issue, if there is any problematic behavior.