Genomic DNA from three Clostridium difficile strains was analyzed by PCR for DNA sequences encoding toxin A (tcdA) and toxin B (tcdB). Toxigenic control strain VPI 10463 possessed tcdA, tcdB, and an open reading frame (tcdE) between these two genes, whereas nontoxigenic control strain 85 lacked each of these genetic determinants. However, strain M90, also a nontoxigenic strain, was found to possess tcdA, tcdB, and tcdE. Normally the presence of toxin genes is associated with toxigenicity. Analysis of tcdA and tcdB mRNA revealed toxin gene transcription in strains VPI 10463, 23 (a mildly toxigenic strain), and M90, but not in strain 85. However, for strain M90, tcdA and tcdB mRNA was at the lower limit of detection, whereas mRNAs encoding tcdA and tcdB were easily detected in strains VPI 10463 and 23. Low levels of toxin gene transcription is the probable cause of M90's lack of toxigenicity.