Sturgeons are archaic fishes phylogenetically distinct from Teleosts. They represent an important niche for aquaculture, particularly for the production of caviar and high quality fillets, while many natural populations in various world areas are today threatened by extinction. Knowledge of the sturgeon genome is limited, as it is the case of many other species of interest for fishery, aquaculture and conservation. Sequences from non-normalized libraries of skin and spleen of the American sturgeon (A. transmontanus) produced in our laboratories were analysed via a bioinformatic procedure, and compared to similar resources available for three Teleost species. Data collected during the analyses were stored in a database - the Sturgeon database (db) - that can be queried via a web interface. The Sturgeon db contains a total of 16,404 sequences from Acipenser transmontanus, Ictalurus punctatus, Salmo salar and Takifugu rubripes, each specie being represented by expressed sequence tags (ESTs) from skin and spleen. Data contained in the database are the results of a number of analyses that mostly focus on sequence annotation and intra- and inter-species comparison. Putative SNP sites, tandem repeats, and sequences matching known protein patterns and motifs were also identified. The Sturgeon db is by now the only online resource dedicated to the analysis of A. transmontanus EST sequences, and represents a starting point for the investigation of the genome of sturgeons from a physiological perspective; it will be used to identify polymorphic markers to study, for example, fish pathologies or to survey fish disease resistance, and to produce gene expression arrays. Introduction of sequences from other species in the analysis pipeline allowed inter-species comparisons of transcripts distribution in Gene Ontology categories, as well as orthologs identification, despite the high sturgeon phylogenetic distance from other fish species. As a result of the EST analysis procedure, 1058 sturgeon novel unigenes were identified.