Stem cells reside in a highly specialized, complex microenvironment that is known as the stem cell niche. The stem cell niche can be described as an anatomically defined space where the stem cell is localized and nourished and stem cell quiescence, proliferation and differentiation are maintained. Tissue engineering aims to imitate the stem cell niche to (I) induce a directed differentiation, (II) maintain the self-renewal capacity or (III) find a regulated balance between self-renewal and differentiation. Mesenchymal stem or stromal cells (MSC) can differentiate in three-dimensional collagen gels into functional osteoblasts when subjected to a phosphate-rich cultivation medium. Furthermore, they acquire a prosynthetic, matrix remodeling, contractile phenotype. Medial artery calcification in patients with chronic kidney disease also proceeds through intramembranous ossification resulting from osteoblast-induced calcification of the collagen extracellular matrix. Thus, the influence of uremic cultivation conditions as a pathophysiological stimulus on MSC and endothelial cells was analyzed with special regards to matrix remodeling, vascularization and calcification. The results showed that BMP-2/4 mediated MSC (mal)differentiation into osteoblasts with acquired matrix remodeling phenotype and loss of proangiogenic capacity. These studies have led to the conclusion that uremia has detrimental effects on the stem cell niche and promotes the continuous calcification by osteogenic (mal)differentiation. In summary, recent studies have shown the conducting and regulating effect of the stem cell niche under physiological conditions that can be applied and mimicked for tissue engineering applications. However, under pathological conditions the stem cell niche can have detrimental effects on stem cell function and can promote disease progression.