To investigate if brain necrosis induction correlates with regions of high linear energy transfer (LET) for proton radiation therapy treatments with partial brain involvement for central nervous system (CNS) and head and neck (H&N) patients. Fifty patients irradiated between 2004-2016 with CT image changes indicative of brain necrosis after irradiation were collected. For each patient, the necrotic region was contoured using MRI imaging. To obtain the LET distributions in the patients, treatment plans were recalculated using Monte Carlo simulations with TOPAS version 3.0.1. For each patient, voxels in the necrotic region were dose-matched with randomly selected voxels in the non-necrotic region of the brain and analyzed for a correlation of LET and occurrence of necrosis. In addition, a simplified relative biological effectiveness (RBE) model assuming a linear increase of RBE with LET was applied. A multilevel mixed-effects logistic regression was used to assess the impact of LET, dose, and tumor site on voxel-based necrosis. The probability of voxel necrosis was statistically significantly associated with increasing dose (p<0.0001) and tumor site (i.e., for the same dose H&N voxels are significantly more likely than CNS voxels to develop necrosis, p<0.0001). The LET was not associated with necrosis when adjusted for dose and tumor site, p=0.7. However, there are significant differences between patients (I2 statistics = 99.4%, p<0.0001) with some patients having significantly higher mean LET values in the necrotic regions (e.g., average LET 5.0 keV/μm vs 3.4 keV/μm, p<0.0001) while others having no difference or even lower LET values in the necrotic regions (e.g., 3.3 keV/μm vs 3.7 keV/μm, p<0.0001). The average difference in LET for dose-matched voxels was less than 0.2 keV/μm for the CNS and H&N cohorts as well as the average over the entire patient cohort. Selecting only high dose voxels (> 50 Gy) or the hottest 20 or 100 voxels also did not reveal any correlation between LET and onset of necrosis. The largest difference in LET was 1.8 keV/μm. The average difference in RBE over the patient cohort was less than 0.5 Gy(RBE), however, 13 patients had over 1 Gy(RBE) higher biological dose in the necrotic region and two patients showed a difference of over 4 Gy(RBE). Overall, we did not find any evidence for higher LET in necrotic voxels compared to non-necrotic voxels with the same dose (p=0.7). The LET (or RBE) variation alone cannot explain the induction of brain necrosis and there are other risk factors that need to be accounted for. Nevertheless, for some patients, high LET regions correlated with the necrotic region. These patients may benefit from LET optimization.