Technical Abstract: The wheat Expressed Sequence Tags (ESTs) in the GenBank totaled 1,051,465 ESTs offer a platform for deciphering differentially expressed genes in wheat. These ESTs are clustered into 41,256 UniGene sets that are non-redundant gene-oriented clusters. This study presented means to efficiently utilize this public database for gene expression profiling of wheat developing-seed. Using a data mining tool called Digital Differential Display (DDD), thirteen pair-wise comparisons were performed on seven cDNA libraries from five cultivars at various developing stages. DDD revealed 46 seed-specific UniGene sets, excluding the well characterized seed storage proteins. Additionally, developmentally-specific UniGenes were identified. Some of these genes encode for proteins such as purothionins, serpins, alpha amylase-inhibitor enzymes, lipid transfer proteins in addition to novel gene sequences. Specifically, the wheat serpin and ß -purothionin precursor were found to be expressed at higher levels in hard varieties than soft varieties. This study supports the starting premise that by implementing in-silico analysis of the wheat UniGene database, it is possible to rapidly create transcriptional profiles of known and novel genes in specific tissues.