Potential users of cryopreserved insect germplasm have expressed concern that the vitrification process, including the chemical permeabilization and post storage recovery procedures, may have an effect on overall insect quality. As part of our attempts to resolve this concern, we have initiated a study examining differential gene expression in cryopreserved and non-cryopreserved Mexican fruit flies. Profiling differential gene expression has become increasingly popular means to identify the molecular effects of stressors which, in the case of our insect embryo cryopreservation protocol, includes the potential for cold shock, osmotic stress, chemical toxicity and oxygen deprivation. In this study, adult males reared from embryos cryopreserved using the technique of Rajamohan et al. [2003] and untreated controls were used for mRNA isolation. Primary screening for differentially expressed genes was carried out using a modified differential display technique. The majority of the generated gene fragments showed similar expression in both the cryopreserved and untreated flies. Thirteen PCR amplicons of possible differentially regulated genes were isolated and cloned. The BlastX software was used to screen the GeneBank sequence repository for homology. Putative genes displaying down-regulation were identified as ATP synthase, ribosylation factor, ribosomal protein L-4 and L-18, unspecified ras, growth inhibitor and imaginal disc growth factor 4 genes. Conversely, a gene involved in flight muscle development showed up-regulation in the cryopreserved flies. We are affirming these results by Northern blot analysis and are continuing to screen for other differentially expressed genes in cryopreserved insects.