Abstract: Described is a method of polymerase chain reaction (PCR) analysis of polymorphisms in the 16s-23s intergenic spacer region of Clostridium difficile (“PCR ribotyping of Clostridium difficile”) comprising the use of a 16s primer corresponding to bases 1450 to 1501 of the 16s ribosomal RNA gene of C. difficile and a 23s primer corresponding to bases 1 to 50 of the 23s ribosomal RNA gene of C. difficile, characterized in that the PCR is performed with a labeled 16s primer and an unlabeled 23s primer and that the DNA molecules provided by the PCR are separated by size using capillary gel electrophoresis.