Cultured plant cells have high potential in providing efficient and low-cost molecular farming systems for the large-scale production of commercially valuable recombinant proteins. As an initial aim at establishing an efficient expression system for suspension-cultured cells of food crops, we first obtained 1411 expressed sequence tags from a sweet potato cDNA library of exponential phase cells, and assembled them into 156 contigs and 1039 singletons. Five ESTs were selected as the most significantly abundant genes. These were transcripts for a cell wall development protein (cinnamyl alcohol dehydrogenase), a carbohydrate metabolite protein (glyceraldehyde-3-phosphate dehydrogenase), and a cell cycle regulator protein (small GTP binding protein Ran), as well as inorganic pyrophosphatase and cyclophilin. Comparisons were then made with the root and leaf EST libraries of sweet potato. Northern blot and RT-PCR analyses revealed that these five genes were strongly expressed in the suspension cells but not in the roots and leaves, thereby supporting the data obtained from the comparative analysis. This is the first reported comparison of the various EST libraries isolated from different cell types of the same plant species. These genes can now contribute to an applicable promoter for devising an efficient expression system from suspension-cultured cells.