Abstract PURPOSE Glioblastoma (GBM) is a heterogeneous brain tumor. Standard treatment constitutes surgery, chemo-radiation, and chemotherapy. After surgery, the resected tissue is analyzed under a microscope by neuropathologists to identify distinct histological hallmarks. However, visual analysis of GBM pathological features on Hematoxylin and Eosin (H&E)-stained slides is subjective, time-consuming, and more importantly, requires wide expertise. We present a hierarchical deep learning-strategy to automatically segment distinct GBM hallmarks that first distinguishes necrosis (NE) from cellular tumor (CT), and subsequently, segments regions of microvascular proliferation (MV) and pseudo-palisading cell patterns (PC) within the CT region, on digitized H&E slides. METHODS We employed n=541 publicly available studies including IvyGap (n=41), and TCGA (n=500). For the IvyGap cohort, expert-driven segmentations of CT, NE, MV and PC were available. We randomly employed n=21 slides from 4 patients for training, n=5 slides from 2 cases for validation, and n=2 slides from 2 cases for testing. We employed an EfficientNet model using ~600 patches of 224×224 pixels of NE and CT sampled for every slide. For semantic segmentation of MV and PC, we separately trained two EfficientNet-UNet models trained on ~200 squared-patches of 1792 and 896 pixels size, respectively. RESULTS Our hierarchical deep learning model on the IvyGap cohort achieved an accuracy of 96%, with an area under the curve (AUC) of 98% for distinguishing necrosis from non-necrotic (i.e. CT) regions. For segmenting PC and MV within the non-necrotic regions, our DL models achieve a dice score of 0.69 and 0.77, respectively. Additionally, the segmentation results for each of the pathological attributes were also generated and vetted for the TCGA cohort. CONCLUSION We developed a hierarchical model for automatic segmentation of NE, CT, and MP and PC in H&E-stained Glioblastoma images which could reduce cost, time, and effort in annotating these pathological phenotypes, for quantifying the GBM micro-environment.