A nested polymerase chain reaction was utilized to successfully detect the type B botulinum neurotoxin gene of Clostridium botulinum in feces from a 6-month-old patient, who had already been diagnosed with type B infant botulism by mouse bio-assay. This method of rapid diagnosis without enrichment culture of feces can be applied to other types of toxins in the use of the type-specific primers. Further investigations, however, are required to define the sensitivity and specificity of the method.