show Abstracthide AbstractBackground Rainbow trout, Oncorhynchus mykiss, is an important worldwide aquaculture species and in addition to its commercial interest, it is also a model research organism of considerable scientific importance. Because of the lack of a currently available whole genome sequence in that species, genomic analysis have been often slowed down by the limited knowledge available on it transcriptome. Using next generation sequencing (NGS) technologies we aimed to complement this knowledge by providing new tissue-specific cDNA repertoires from different rainbow trout tissues using the 454-Titanium technology. Results Several non-normalized cDNA libraries were constructed from testis, ovaries, brains and gills rainbow trout samples and these different libraries were sequenced in 10 separate half-runs of 454-Titanium. Overall we produced a total of 3 millions good quality sequences (testis: 1.234.260, ovaries: 738.510, brains: 481.363 and gills: 613.223) with an average size of 328 bp representing more than 1 Gb of expressed sequence information.