Intralesional fibrous septum (IFS) generally is considered a reactive tissue in chordoma; however, little is known about its significance. We studied 122 chordomas for IFS using immunohistochemical techniques and compared IFS and lobular growth patterns (LGPs) formed by IFS with clinicopathologic parameters. Seventy-nine tumors (64.8%) revealed IFS. However, IFS frequently was infiltrated and interrupted by tumor cells with increased expression of proteases; only 33 (42%) of 79 tumors had LGP. In non-skull base chordomas, IFS and LGP were associated with nuclear pleomorphism, a previously described prognostic indicator, mitosis, and the MIB-1 labeling index, indicating a role of IFS and LGP in tumor growth or progression. Paradoxically, patients without LGP tended to have a worse prognosis than those with LGP. We believe that IFS exerts diverse influences on chordoma; however, invasion of IFS leading to loss of the LGP indicates advanced stages of tumor development, possibly predicting an unfavorable prognosis in chordoma.