“Small intestinal submucosa” (SIS) is a natural degradable biomaterial derived from the small intestine of vertebrates. Porcine SIS has been widely used in repairing various tissues and organs, especially in nervous tissues because intrinsic autonomic nerve plexuses are included in submucosal layer. However, little is known about active neurotrophic factors in this material. In this study, we proposed a method to prepare an extract from decellularized SIS and to identify and characterize the major neurotrophic factors in it. Decellularized SIS extract was obtained by sequential procedures: mechanical disassociation, degreasing, enzyme digestion, freeze-drying, freezer-milling, extracting, concentrating, and filtering. Contamination with cellular components in the SIS extract was evaluated by hematoxylin and eosin (H&E) staining and the content of genomic DNA. Major neurotrophic factors in SIS extract was assessed quantitatively by ELISA. The effects of SIS extracts on cells were evaluated by observation of neurite outgrowth from PC12 cells. Decellularized SIS extract was obtained successfully by the proposed method and no cellular component was found within it. Brain-derived neurotrophic factor (BDNF), erythropoietin (EPO), glial cellderived neurotrophic factor (GDNF), nerve growth factor (NGF), and platelet-derived growth factor (PDGF) were identified and characterized form SIS extract. The bioactivity of SIS extract was assessed in terms of neurite outgrowth from PC12 cells. In summary, we prepared a decellularized extract from porcine SIS and identified major neurotrophic factors present in it. SIS extract also had bioactivity with PC12 cells. From these results, we conclude that SIS may be useful to repair or improve nervous system function.