The starch and protein in wheat (Triticum aestivum L.) endosperm provide 20% of the calories eaten by humans and were heavily selected for during domestication. We examined the main storage products and gene expression patterns that may embody compositional differences between two wild species Aegilops crassa and Aegilops tauschii and cultivated bread wheat. The storage product profiles differed significantly with T. aestivum accumulating twice as much carbon as the wild species, while the latter had 1.5 to 2-fold more total nitrogen per seed. Transcriptional analyses of endosperms of similar fresh weight were compared using a cDNA macroarray. Aegilops tauschii, and especially Ae. crassa had stronger hybridizations with storage protein sequences, but while there were differences in transcripts for starch biosynthetic genes, they were less dramatic. Of these, we cloned the Starch Branching Enzymes (SBE) IIa promoter region and the genomic clone of the Brittle-1 (Bt1) ADPglucose transporter. While Ae. crassa SBEIIa sequence was more divergent than that of Ae. tauschii's compared to bread wheat, there were no sequence polymorphisms that would explain the observed expression differences in Bt1 between these species. Furthermore, while there were nucleotide differences between Bt1 in Ae. crassa and bread wheat, they were synonymous at the amino acid level. Some of transcriptional differences identified here, however, deserve further examination as part of a strategy to manipulate wheat starch and protein composition.