This study was conducted at Ngudi Makmur farmer group Samiran village, Parangtritis village, Kretek subdistrict, Bantul regency, Special Region of Yogyakarta which was a productive shallot farmer group and had the most widely warehouse storage of shallot seeds in Yogyakarta. Less lack of shallot seeds caused the increasing of shallot price, because the level of cultivation was low, so the Goverment attempted to stabilize the price by building warehouse storage of shallot seeds. The purpose of this study was to find out the factors that influence the farmer’s decision in saving the shallot seeds and toinvestigate the different of cost and profit between saving the shallot seeds in the warehouse and in the house. The respondent of study was selected by using proposional random sampling with the number of respondent were 47 farmers which was consisted of 28 farmers were saving their shallot seeds in warehouse and 19 farmers were saving it in the house. The data was analyze by using binary logistic regression and continued by analyzing cost and profit. The result showed that the wide of house, the wide of personal warehouse, the wide of dried place, and perception have a significant effect on the farmer’s decision in saving their shallot seeds. (1) The wider farmer’s house, the more likely they save the seeds in the warehouse; (2) The wider farmer’s personal warehouse,the more likely they save the seeds in the house; (3) The wider dried place, the more likely they save they save the seeds in thehouse; (4) and better farmer’s perception on the group warehouse, the most likely they save the seeds in the warehouse. Meanwhile, from the cost and profit analyze showed that kept the shallot seeds in house were had more profit.