Our previous study of a gastrointestinal autonomic nerve tumor with skeinoid fibers (SF) using the quick-freezing and deep-etching method, suggested that the distance between one radix and a neighboring radix (DRNR) in pre-existing meshwork structures around the tumor cells is consistent with the periodicity of the SF. Therefore, measurement of the DRNR in the meshwork could clarify the significance of the pericellular matrix for SF development. In the present study, we analyzed the meshwork in three cases of gastrointestinal stromal tumor (GIST), which showed different immunohistochemical stainings, but confirmed to have smooth muscle differentiation (SMD) by immunohistochemistry and/or electron microscopy. The DRNR from the three cases of GIST showed similar histogram patterns (a peak of 20-30 nm, mean values of 28.02, 25.74 and 26.45 nm), which were significantly shorter than the periodicity of SF (a peak of 40-45 nm, mean value of 42.14). Although we need further studies with additional GIST cases, we speculate that the pericellular matrix of GIST with SMD is not suitable for SF development.