The need for rapid diagnosis of Clostridium difficile (C. difficile) associated infection in a clinical microbiology laboratory has provided the stimulus for new diagnostic tests and testing protocols. A twotest algorithm has been proposed using assays such as Quik Chek Complete, which detects both C. difficile glutamate dehydrogenase (GDH) and C. difficile toxins A and B, followed by reflex testing of samples having inconclusive results (GDH positive and toxin negative) with PCR for identification of toxin gene specific DNA. The goal of this study was to compare the outcome and efficiency of PCR assays, BD GeneOhm and GeneXpert, for detecting C. difficile toxin B gene in samples that have tested indeterminate for C. difficile by the Quik Chek Complete test. Over a three-month period, a total of 41 cases tested indeterminate by Quik Chek Complete test and were retested by the aforementioned PCR assays. Out of the 41 samples, 36 had matching results in both assays; 19 negative samples and 17 positive samples. In terms of efficiency, GeneXpert was user-friendly and had a turnaround time (TAT) of 45 minutes with two-minute specimen processing compared to BD GeneOhm which had a TAT of 75 to 90 minutes.