To identify genes related to initiation of storage root development in sweet potato, a cDNA library was constructed with early stage storage roots (0.3-1 cm in diameter). Single-pass sequences of the 5' ends of 2859 sweet potato cDNA clones were assembled into 483 clusters and 442 singletons. Comparison of sweet potato expressed sequence tags (ESTs) to nodulation/tumorigenesis-related sequence databases (nodule-, tumor-, potato tuber- and development-related sequences) revealed that homologs of 39 sweet potato EST sequences potentially involved in gene regulation, signal transduction and development were present in at least one of the nodulation/tumorigenesis-related sequence databases. Northern blot analyses of these 39 sequences identified 22 differentially expressed genes in early stage storage root and fibrous root. These differentially expressed genes will be potential candidates for research to elucidate the molecular processes related to sweet potato storage root induction.