Individuals with xenomelia identify with an amputated rather than with their physically complete, healthy body. They often mimic amputees and show a strong admiration of and sexual attraction towards them. Here we investigated for the first time empirically whether such unusual preference for amputated bodies is present also on an implicit level. Using the well-validated Implicit Association Test we show that individuals with xenomelia manifested a stronger implicit and explicit preference for amputated bodies than a normally-limbed control group and a group of involuntary amputees did. Interestingly, the two latter groups did not differ in their implicit and explicit preference for complete versus amputated bodies. These findings are an important step in understanding how deeply rooted attitudes about a socially normative body appearance may be influenced by a developmentally disordered experience of one's own bodily self. We conclude that this is the first behavioral evidence demonstrating a conflict of self-identification on an implicit level and this enriches current understandings of xenomelia as a primarily neurological disorder.