Objective: Chronic hypoxia exists in many diseases, including cancer. The subject of our study is analysis of molecular pathways affected in the chronically hypoxic mouse brain. Materials and Methods: Using the emPAI protocol, we performed a quantitative proteomic approach to characterize the global proteome in the mouse brain exposed to 7% O2 for 48 hours. Results: Utilizing the emPAI protocol to estimate protein abundance and assign molar concentrations to all proteins, we were able to identify 33 proteins with significant changes in their expression. Conclusion: Deregulated proteins were mainly involved in cell metabolism, apoptosis, Ca2+ signaling, pentose phosphate pathway, 14-3-3 protein mediated signaling cascades and protein degradation. The obtained data will provide some clues for understanding mechanisms with which cells respond and adapt to chronic hypoxia.