Clostridium difficile remains the leading cause of nosocomially acquired diarrhoea. C. difficile usually exhibits resistance against beta-lactam antibiotics, whereas susceptibility to other drugs may vary. This study investigated the antimicrobial susceptibility of C. difficile to different antibiotics over a period of time and characterizes molecular mechanisms for resistance. One hundred and seventy-three toxigenic and 19 non-toxigenic C. difficile strains, recovered from patients in two university hospitals in Germany between 1986 and 2001, were investigated for their susceptibility to erythromycin, clindamycin, moxifloxacin, vancomycin and metronidazole employing the Etest. The genetic background for resistance was analysed using PCR and DNA sequencing. All strains were susceptible to vancomycin and metronidazole. Resistance to erythromycin, clindamycin and moxifloxacin was found in 27%, 36% and 12% of the tested strains, respectively. High-level resistance (MIC > 128 mg/L) against erythromycin and clindamycin was detected in 25% of the strains tested. Thirty-four of the macrolide-lincosamide-streptogramin B (MLS(B))-resistant strains carried the erythromycin resistance methylase gene. The results indicate an increase in the prevalence of resistance to MLS(B) and fluoroquinolone antibiotics in C. difficile. Fluoroquinolone resistance is associated with resistance to MLS(B) antimicrobials.