We evaluated the performance of a commercial PCR kit for the detection of Clostridium difficile toxin A and B genes directly in patient stool specimens. Results will be compared with data from these traditional tests for diagnosis of C. difficile gastrointestinal disease: toxigenic culture, cytotoxin assay, and ELISA for toxins A and B. We tested 144 stool specimens by all methods. We are currently waiting for data from the ELISA tests which were performed at Hennepin County Medical Center and for results from chart reviews for specimens that gave conflicting results before the manuscript can be completed and submitted for publication.