This study describes the development of a cost-effective, multiplex Loop-Mediated Isothermal Amplification (LAMP) method for detection of toxigenic Clostridioides difficile from diarrheal stools and presumptive identification of the NAP-1 strain. The diagnostic values for the new method were as follows: 100.0% specificity, 95.0% sensitivity, 100% positive predictive value, and 97.0% negative predictive value as compared to real-time PCR. The estimated cost per test is Cdn$ 3.75 and which is significantly less than commercial assays. The average turn-around-time from set-up to detection is 1.5 h. The LAMP method described here is a cost-effective, quick and highly sensitive test which can be implemented in a clinical laboratory to assist clinicians in establishing the diagnosis of CDI and to indirectly determine the presence of the hypervirulent epidemic binary toxin producing NAP1 strain.