During growth,C. botulinumis always exposed to different environmental changes, such as temperature increase, nutrient deprivation, and pH change; however, its corresponding global transcriptional profile is uncharacterized. This study is the first description of the genome-wide gene expression profile ofC. botulinumin response to heat shock stress. Under heat stress (temperature shift from 37°C to 45°C over a period of 15 min), 176C. botulinumATCC 3502 genes were differentially expressed. The response included overexpression of heat shock protein genes (dnaKoperon,groESL,hsp20,andhtpG) and downregulation of aminoacyl-tRNA synthetase genes (valS,queA,tyrR, andgatAB) and ribosomal and cell division protein genes (ftsZandftsH). In parallel, several transcriptional regulators (marR,merR, andompRfamilies) were induced, suggesting their involvement in reshuffling of the gene expression profile. In addition, many ABC transporters (oligopeptide transport system), energy production and conversion related genes (glpAandhupL), cell wall and membrane biogenesis related genes (fabZ,fabF, andfabG), flagella-associated genes (flhA,flhM,flhJ,flhS, andmotAB), and hypothetical genes also showed changed expression patterns, indicating that they may play important roles in survival under high temperatures.