Provided is an apparatus for generating an identification key by a probabilistic determination of a short occurring between nodes constituting a circuit, by violating a design rule provided during a semiconductor manufacturing process. The identification key generating apparatus may include an identification key generator to generate an identification key based on whether a contact or a via used to electrically connect conductive layers in a semiconductor chip shorts the conductive layers, and an identification key reader to read the identification key by reading whether the contact or the via shorts the conductive layers.