Hirschsprung disease (HSCR) is a congenital disorder caused by a failure of neural crest cells to migrate, proliferate, and/or differentiate during the enteric nervous system (ENS) development. The requirement of the NTF-3/TrkC signaling for the proper development of the ENS, together with the evidences presented by animal models, led us to investigate the involvement of NTF-3 gene in HSCR. We performed both a mutational screening of NTF-3 and a complete evaluation of 3 polymorphisms as genetic susceptibility factors for HSCR. We identified a novel sequence variant, G76R, present in 2 different patients and absent in controls. We postulate that this variation could generate a lack of mature functional NTF-3 proteins in neural crest cell precursors; thus, altering the NTF-3/TrkC signaling pathway and influencing in the adequate ENS development. Although these results do not provide complete assurance of the involvement of this gene in HSCR, given the polygenic nature of the disease and its etiology, investigation of the genes encoding protein members of the signaling pathways governing the ENS development could provide new key findings in the elucidation of this complex disease.