To date, a total of 68 isolates of Clostridium difficile have been collected from a community hospital and the NIH Clinical Center and tested for resistance to fluoroquinolones. Ciprofloxacin and moxifloxacin were used to identify fluoroquinolone resistant isolates. The resistant rate of NIH C. difficile isolates to Ciprofloxacin alone was 58%(14/24) and resistance to both ciprofloxacin and moxifloxacin was 17% (4/24). The resistance rates in isolates from the community hospital were 16% (7/44) and 70% (31/44) respectively. Preliminary sequencing data from the QRDRs of gyrA and gyrB genes of selected sensitive and resistant isolates has revealed point mutations in gyrA of these fluoroquinolone resistant isolates.