The hematopoietic microenvironment, also referred to as hematopoietic niche, is a functional three-dimensional (3D) unit of the bone marrow (BM) that planar culture systems cannot recapitulate. Existing limitations of 2D protocols are driving the development of advanced 3D methodologies, capable of superior modeling of the native organization and interactions between hematopoietic cells and their niche. Hereafter we describe the use of a 3D perfusion bioreactor for in vitro generation of human hematopoietic niches. The approach enables the recapitulation of the interactions between hematopoietic stem and progenitor cells (HSPCs), mesenchymal cells (MSCs), and their extracellular matrix in a 3D relevant setting. This was shown to support the functional maintenance of blood populations, self-distributing in the system compartments depending on their differentiation status. Such 3D niche modeling represents an advanced tool toward uncovering human hematopoiesis in relation to its host microenvironment, for both fundamental hematopoiesis and personalized medicine applications.