Carrot is one of the useful crops used abundantly in cooking in Western as well as Asia regions such as China and Korea. However, seed coats have hairs which should be removed to increase germination rate. Furthermore, because of seed hairs, farmers face several additional losses, such as time consumption, manpower, capital and so on, for seed handling. To prevent these problems, study of gene related hair formation using short-hair seed lines is required. We analyzed genes related to hair formation from seed through expressed sequenced tag (EST) profiling, based on the fact that the development of carrot seed hair is related to cellulose synthesis pathway in secondary cell wall synthesis stage. To study the gene expression related to hair formation of the carrot seed, a cDNA library was constructed by using the early maturation stage of the short-hair line (659-1) and hairy seed line (677-14). In short-hair (659-1) and hairy seed (677-14) lines, results from of EST profiling through BLASTX search analysis using the NCBI database showed that 172 and 224 unigenes had significant homology with known protein sequences, whereas 233 and 192 unigenes were not, respectively. All ESTs were grouped into 16 categories according to their putative functions. Twenty nine unigenes among all ESTs were considered to be genes regulating seed hair development from cellulose synthesis pathway during secondary cell wall synthesis stage; in results, 14 unigenes related to seed hair development were found only in hairy seed line.