We aimed to determine how often Clostridium difficile toxin gene PCR assay (CDPCR)-negative patients were appropriately removed from single room contact isolation. Hospital databases were used to collect information on glutamate dehydrogenase (GDH)-positive, toxin-negative inpatients (February-April 2015). Of 60 CDPCR-negative patients, only two (3%) were removed from single room isolation. At least 36% of 53 CDPCR-positive results did not influence bed management. In conclusion, identification of C. difficile toxigenic status did not impact significantly on decisions whether to continue single room isolation. Cost-benefit analysis should be undertaken before CDPCR testing is introduced.