Genotyping of bacterial strains via pulsed-field gel electrophoresis has to be considered an important tool for epidemiological investigations in food hygiene as well as in other areas. Yet, a major disadvantage of this method is its long duration. Therefore, rapid procedures for DNA isolation and restriction are being sought. One such protocol was modified and further shortened to two days. This short protocol was used for macrorestriction analysis of 34 strains of 25 different Clostridium species. Parallel analyses were performed using a conventional 5-day protocol in order to compare the long and the short method by running the DNA samples obtained via both protocols on the same gel. In the case of nine strains, none of the two methods yielded satisfactory results, whereas for three strains the long protocol proved to be preferable to the short one. Comparable results were obtained using both methods in the case of 22 strains belonging to 17 different Clostridium species.