Saliva of Aedes aegypti contains a complex array of proteins essential for both blood feeding and pathogen transmission. A large numbers of those proteins are classified as unknown in regard to their function(s). Understanding the dynamic interactions at the mosquito-host interface can be achieved in part by characterizing mosquito salivary gland gene expression relative to blood feeding. Towards this end, we developed an oligonucleotide microarray representing 463 transcripts to determine differential regulation of salivary gland genes. This microarray was used to investigate the temporal gene expression pattern of Ae. aegypti salivary gland transcriptome at different times post-blood feeding. Expression of the majority of salivary gland genes (77-87%) did not change significantly as a result of blood feeding, while 8 to 20% of genes were down-regulated and 2.8 to 11.6% genes were up-regulated. Up-regulated genes included defensins, mucins and other immune related proteins. Odorant-binding protein was significantly down-regulated. Among unknown function proteins, several were up-regulated during the first three hours post-blood feeding and one was significantly down-regulated. Quantitative real-time RT-PCR was used to substantiate differential expression patterns of five randomly selected genes. Linear regression analysis revealed a high degree of correlation (R2 > 0.89) between oligonucleotide microarray and quantitative RT-PCR data. To our knowledge, this is the first study to investigate differential expression of the Ae. aegypti salivary gland transcriptome upon blood feeding. A microarray provides a robust, sensitive way to investigate differential regulation of mosquito salivary gland genes.