Using the polymerase chain reaction (PCR)-select subtractive cDNA hybridization technique, 18 different genes were isolated from a permethrin-treated versus acetone-treated Aedes aegypti subtractive library. Quantitative PCR (QPCR) results showed that 8 of the 18 gene's transcriptional levels in permethrin-treated Ae. aegypti were at least two-fold higher (ranging from 2.6 ± 0.5 to 4.8 ± 0.2) than that in acetone-treated Ae. aegypti. These eight genes include three functionally known genes (cytochrome c oxidase subunit III, NADH2 dehydrogenase, deltamethrin resistance associated protein), three functionally unknown genes (Ae. aegypti putative 16.9-kDa secreted protein, Anopheles gambiae ENSANGP00000019508, Cryptococcus neoformans hypothetical protein CNE05340), and two novel genes. Transcriptional levels for 11 of the 18 genes were induced significantly higher by permethrin than by fipronil (P < 0.05). Our results suggest that subtractive cDNA hybridization and QPCR are powerful techniques to identify differentially expressed genes in response to pesticide treatment.