The use of autografts, as primary cell and tissue source is the current gold standard approach to treat critical size bone defects and non-union defects. The unique mixture of the autografts, containing bony compartments and bone marrow (BM), delivers promising results. While BM mesenchymal stromal cells (BM-MSCs) still represent a major target for various healing approaches in current pre-clinical research and respective clinical trials, their occurrence in the human BM is typically low. In vitro expansion of this cell type is regulatory challenging as well as time and cost intensive. In comparison to marginal percentages of resident BM-MSCs in BM, BM mononuclear cells (BM-MNCs) contained in BM aspirates, concentrates and bone autografts represent a readily available abundant cell source, applicable within hours during surgical procedures without the need for time consuming and regulatory challenging cell expansion. This benefit is one reason why autografting has become a clinical standard procedure. However, the exact anatomy and cellularity of BM-MNCs in humans, which is strongly correlated to its unique mode of action and wide application range, remains to be elucidated. The aim of this review was to present an overview of the current knowledge on these specific cell types found in human BM, emphasize the contribution of BM-MNCs in bone healing, highlight donor site dependence and discuss limitations in current isolation and subsequent characterization procedures. Hereby the most recent and relevant examples of human BM-MNC cell characterization, flow cytometric analyses and findings are summarized, with a strong focus on bone therapy.