Rationale: Macrophages are innate immune cells presenting a strong phenotypic plasticity and deeply involved in tissue homeostasis. Oxygen environmental tension is a physical parameter that could influence their polarizations. In this study we use time-of-flight secondary ion mass spectrometry (TOF-SIMS) to describe how various polarizations are modified by a low oxygen exposure. Methods: TOF-SIMS experiments were performed using an IONTOF ToF-SIMS 5–100 (ION-TOF GmbH, Munster, Germany). Analysis was performed using a pulsed 25 keV Bi3+ beam, sputtering was performed using a 250 eV Cs beam. Cells were fixed by paraformaldehyde before TOF-SIMS analysis. Results: Multivariate analysis of the TOF-SIMS spectra provided ion species associated with the exposure of macrophages to low oxygen concentration. We were able to obtain some species, specific of a particular polarization, advocating for the use of macrophages as reporter cells of oxygen tension in tissues. Conclusions: Our study demonstrates that macrophage molecular signature to low oxygen environment is dependent on their polarization. TOF-SIMS shows the clear capability to produce species revealing this exposition. This result opens the way to the use of TOF-SIMS as a tool to explore hypoxia in human tissues. Copyright © 2017 John Wiley & Sons, Ltd.