Clostridium difficile is the most common pathogen causing antibiotic-associated diarrhea. Antibiotic therapy also favors the development and the epidemic spreading of multiresistant strains. In this present retrospective study clinical isolates from the University of Saarland Medical Center and of other German isolate referring hospitals were characterized by genotyping and antibiotic resistance testing. The most prevalent strains were ribotypes 001 (18%), 014 (16%) and 027 (15%). Sensitivity to metronidazole and vancomycin was demonstrated for 99.7 % of the clinical isolates independent of the genotype. Of the isolates 96 % were rifampicin susceptible; however, significantly more cases of rifampicin resistance were found among 027 strains (12 %). Of the isolates 58% were clarithromycin sensitive and 57% moxifloxacin sensitive. In contrast to the various sporadic genotypes the majority of epidemic strains were macrolide or fluoroquinolone resistant (001, 027 and 078); however, discrimination between epidemic strains by antibiotic resistance profiles could not be discerned. A combination of consistent adherence to hygiene management guidelines and to a prudent and rational use of antimicrobials (antibiotic stewardship) may help to reduce the total number of C. difficile infections (CDI) and also the selection of multiresistant strains. On the other hand in the collection of isolates the sensitivity towards the standard oral antibiotic agents used for C. difficile treatment appears to be unimpaired by the global changes of C. difficile resistant profiles.