Brachypodium is an emerging plant species of the Pooideae subfamily, a model plant for Triticeae crops such as wheat and barley, as well as for understanding systems for cellulose biomass production in grass species. We constructed a mixed full-length cDNA library of various tissues of Brachypodium distachyon Bd21 strain by using the biotinylated CAP trapper method. Then, we obtained 79,872 expressed sequence tags (ESTs), which were sequenced from both ends. Each of ESTs was mapped onto the Bd21 genome sequence of Brachypodium based on sequence identity. In total, 75,364 sequences of clones were mapped onto 8,623 annotated loci. PASA analysis was performed to update Brachypodium gene annotation, and then, in total 8,177 loci showed some of the modifications. The RBFL cDNA ESTs aligned with 7,812 loci showed updates of UTR addition, and 459 and 502 loci were modified with extension of coding regions and/or structural rearrangements, respectively. We also analyzed RBFL cDNA ESTS mapped to genomic regions without any Bradi gene models, then 670 non-redundant regions were found as putative new transcribed regions supported by RBFL ESTs. We also performed comparative analyses of the full-length cDNA dataset and those of wheat and barley. To integrate our full-length cDNA information with other related significant information resources, we constructed an integrated database, RIKEN BrahcyFLcDNA DB, which is an information gateway to access the resource. This full-length cDNA resource should be beneficial in accelerating the discovery and functional analysis of genes in Brachypodium distachyon.