Clostridium difficile can be a fatal hospital-acquired infection and its prevalence has increased. Accurate diagnosis of C difficile is essential for patient management, infection control, and for defining its epidemiology. We did a systematic review of commonly used commercial assays for detection of C difficile toxin (CDT) A and B in stool samples. By comparison of detection of CDT in cell culture with or without selective culture for C difficile, the median sensitivities and specificities (IQR) were as follows: Meridian Premier 0.95 (0.86-0.97) and 0.97 (0.95-0.98), TechLab Tox A/B II 0.83 (0.82-0.85) and 0.99 (0.98-1.00), TechLab Tox A/B Quik Chek 0.84 (0.81-0.87) and 1.00 (0.99-1.00), Remel Xpect 0.82 (0.75-0.89) and 0.96 (0.95-0.98), Meridian Immunocard 0.90 (0.84-0.92) and 0.99 (0.98-1.00), and BioMérieux VIDAS 0.76 and 0.93. If the prevalence of CDT A and B in stool samples is relatively low (<10%), the positive predictive value of these assays is unacceptably low (eg, <50% in some circumstances) and will vary depending on the assay and number of samples tested. This low positive predictive value impinges on clinical management, outbreaks, and makes epidemiological data unreliable. To improve diagnosis, we suggest a two-stage testing strategy for C difficile toxin with an initial highly sensitive rapid screening test to identify positive samples that are then confirmed by a reference method.