Temperature is important for mosquito development and physiological response. Several genes of heat shock protein (HSP) families are known to be expressed in mosquitoes and may be crucial in responding to stress induced by elevated temperature. Suppression subtractive hybridization (SSH) was used to identify target transcripts to heat shock treatment in female Aedes aegypti. Subtraction was performed in both directions enriching for cDNAs differentially expressed between a non- heat shock control and heat shock treatment. Heat shock treatment of female Ae. aegypti was carried out for 1 h at 42°C. Clones from differentially expressed genes were evaluated by sequencing. Target transcripts up-regulated by heat shock included five different HSP gene families and 27 other genes, such as cytochrome c oxidase, serine-type endopeptidase, and glutamyl aminopeptidase. Additionally, some novel genes, cytoskeleton and ribosomal genes, were found to be differentially expressed, and three novel up-regulated sequences belonging to a low-abundance class of transcripts were obtained. Up-regulated/down-regulated transcripts from heat shock treatment were further confirmed and quantified by quantitative real-time polymerase chain reaction (PCR). High temperatures can alter the gene expression of a vector mosquito population, and further characterization of these differentially expressed genes will provide information useful in understanding the genetic response to heat shock treatment, which can be used to develop novel approaches to genetic control.