Yersinia pestis, the etiologic agent of plague, must acclimatize itself to temperature shifts between the temperature (26 C) for flea blockage and the body temperature (37 C) of warm-blooded hosts during its life cycle. Here a whole-genome DNA microarray was used to investigate transcriptional regulation upon the upshift of growth temperature from 26 to 37 C in a chemically defined medium. Four hundred and one genes were regulated differentially under the two temperatures. About 39% of these genes were up-regulated at 37 C, whereas 61% were down-regulated. Temperature-induced changes occurred at the level of transcription of genes encoding proven or predicted virulence factors, regulators, metabolism-associated proteins, prophages, and hypothetical proteins. Strikingly, many gene clusters displayed a co-transcription pattern in response to temperature upshift. Our data provided a genome-wide profile of gene transcription induced by temperature shift and should shed light on the pathogenicity and host-microbe interaction of this deadly pathogen.