Glioblastoma is the most common primary brain tumor in adults. With a poor prognosis, its treatment has barely advanced in the last twenty years. High cell densities limit the availability of nutrients/oxygen, leading to necrosis and/or endothelial and microvascular proliferation. However, it exhibits a high capacity for survival, in which glioblastoma stem cells and autophagy may be involved. The objective of this study was to evaluate, among the different histological structures of glioblastoma, the expression of BNIP3 (its product induces autophagy (mitophagy) by direct interaction with LC3B-II) and one of its transcriptional regulators, HIF1A (the O₂-regulated protein promotes adaptation to hypoxia). The results were obtained from the analysis of in situ hybridization (ISH) images in glioblastoma sections, stored in the free database Ivy Glioblastoma Atlas Project. All patients we studied showed high levels of BNIP3 mRNA in the perinecrotic pseudopalisading areas, and medium expression in the vessel walls and even in the infiltrating tumor region. From the pseudopalisading regions around necrosis, BNIP3 transcription decreased significantly as we advanced into the tumor. Interestingly, only some patients showed expression (and in these cases, high expression) of HIF1A in the pseudopalisading formations, although HIF1A was expressed, at variable levels, in the vessel walls. These results indicate anatomy-dependent levels for the mRNA encoding BNIP3 and HIF1A in glioblastoma. Furthermore, they suggest strong mitophagy activation in the pseudopalisading cells, as well as mechanisms regulating BNIP3 mRNA levels independent of HIF1A expression. These mechanisms could be other transcriptional factors, such as E2Fs, FOXO3, TP53, and NFKB, and/or a regulation by stabilization of the HIF1A protein under hypoxia. Our data could also be applied to other brain pathologies, where low oxygen levels contribute to tissue damage.