Contamination of oral pharmaceuticals with microorganisms may lead to deleterious effects on the therapeutic properties of the drug, and may potentially cause injuries to intended recipients. Thirty contaminated samples were detected representing 2% out of 1500 total collected samples. Out of 30 contaminated samples, only six samples (20%) revealed the presence of Clostridium perfringens. The biofilm assay was performed using the Microtiter Plate Method (MTP) for the six of the detected C. perfringens were three isolates biofilm forming. PCR multiplex was done for C. perfringens showed the presence of alpha toxin gene among all species. In spite of the current recommendation for a conventional detection method for Closterium spp., the application of multiplex PCR showed to be more, effective and able to detect Clostridium toxins genes.