Hematopoietic stem cells are maintained and regulated in spatially confined microenvironments within the bone marrow, in which oxygen availability is hypothesized to be very limited. The hypoxic nature of HSC niches is proposed to play a fundamental role in the preservation of fundamental stem cell properties through the induction of a distinct glycolytic metabolic profile in HSCs. Thus, the capacity to determine oxygen levels or cellular oxygenation status in specific tissue locations is essential to deepen our understanding of HSC biology. We here describe a methodology to indirectly quantify the hypoxic status of individual cells in situ within histological sections of bone marrow tissues. We employ the well-characterized nitroimidazole probe, pimonidazole, which acts as an oxygen mimetic and irreversibly incorporates into cellular proteins only under hypoxic conditions. The use of fluorescently labeled antibodies that recognize pimonidazole epitopes then enables the indirect assessment of the intracellular hypoxic status and its relationship to cell positioning within the complex tissue topography of the bone marrow.