Comparison of 12,230 expressed sequence tags (ESTs) of 3' ends of cDNA clones derived from young adults of Ciona intestinalis allowed us to categorize them into 976 independent clusters. When the 5'-end sequences of 10,400 ESTs of the 976 clusters were compared with the sequences in databases, 406 of the clusters showed significant matches ( P < E-15) with reported proteins with defined functions, while 117 showed matches with putative proteins for which there is not enough information to categorize their function, and 453 had no significant sequence similarities to known proteins. The 406 clusters with sequence similarity to proteins with defined functions consisted of 304 clusters related to proteins with functions common to many kinds of cells, 73 related to proteins associated with cell-cell communication and 29 related to transcription factors. Spatial expression of all of the 976 clusters was examined by a newly improved whole-mount in situ hybridization method. A total of 430 clusters did not show distinct in situ hybridization signals, while 122 clusters showed ubiquitous distribution of signals, and 253 clusters showed signals in multiple tissues. The remaining 171 clusters showed signals specific to a certain organ or tissue: 16 showed epidermis-specific expression, 3 were specific to the neural complex, 1 to heart, 6 to body-wall muscle, 94 to pharyngeal gill, 3 to esophagus, 26 to stomach, 1 to intestine and 21 to endostyle. Many of these organ-specific genes encode proteins with no sequence similarity to known proteins. The present analysis thus highlights characteristic gene expression profiles of Ciona young adults and provides not only molecular markers for organs and tissues but also transcriptomic information useful for further genomic analyses of this model organism.