The two-hybrid system is a genetic method to identify proteins that interact with a specific target protein, which is expressed in yeast as a hybrid with a DNA-binding domain. Use of this method entails transforming yeast, both with this DNA-binding domain hybrid and with a library of activation domain hybrids, followed by screening for transcriptional activation of a reporter gene. In addition to proteins that interact with the target protein, a number of false positives are identified. We provide possible explanations for these false positives along with rapid assays to eliminate them.