Several antimicrobial/parasitic peptides are known to be upregulated in mosquitoes upon infection with parasites. The aim of this study was to identify immune-responsive genes in the vector mosquito, Culex quinquefasciatus Say (Diptera: Culicidae) against the human lymphatic filarial parasite, Wuchereria bancrofti (Cobbold) (Spirurida: Onchocercidae). Suppression subtractive hybridization was performed using RNA from filarial infected and non-infected mosquitoes to obtain differentially expressed transcripts, and their identities were confirmed through reverse transcriptase polymerase chain reaction (RT-PCR). Out of 23 clones selected from the suppression subtractive library, three corresponded to antimicrobial peptide genes, defensins, and four corresponded to regulatory serpin peptide genes. RT-PCR using defensin-specific primers and sequencing of the product showed a 284-bp defensin cDNA. Sequence alignment with defensins of the mosquitoes Anopheles gambiae s.s. Giles and Aedes aegypti (L.) showed maximum homology with the former. Similarly, that of serpin-specific primers showed a 406-bp cDNA encoding serpins. Sequence alignment showed maximum homology with that of An. gambiae, as in the case of defensins. Hence, this investigation revealed upregulation of defensins and serpins in Cx quinquefasciatus infected with W. bancrofti. Antimicrobial peptide genes such as defensins may have limited or no specific role in regulating parasite development. Serpins may prove to be facilitating molecules, by regulating melanization of the parasite. However, the exact functions of these molecules in the immune system of the vector mosquito are yet to be investigated.