We have described an approach to fabricate three-dimensional (3D) cell-based structures using functionalized super paramagnetic iron oxide nanoparticles (SPIONs) as patterning agents to guide the assembly of endothelial cell spheroids into 3D patterns using the magnetic forces generated by a prefabricated magnetic template. SPIONs were first uptaken by endothelial cells before they were assembled into uniform-sized spheroids through a home-made robotic spheroid maker. To guide the magnetic spheroids, a unique magnetic template was fabricated using computer-aided design and cut from a magnetic sheet. The spheroids were then guided to the prefabricated magnetic template through the attractive magnetic forces between the SPIONs inside the endothelial cells and the magnetic template. Fusion of endothelial cell spheroids over time while adhered to the magnetic template allowed for the formation of 3D cell-based structures. Subsequent removal of the prefabricated magnetic template left 3-D endothelial cell sheets, which may be stacked to fabricate complicated 3D multicellular tissue structures. To enhance the cytocompatibility, SPIONs were silica-coated before use. At low concentrations, the SPIONs did not adversely affect cell viability, proliferation, and phenotype stability. Light and confocal microscopy showed that endothelial cell spheroids could be reproducibly created with high uniformity. The endothelial cells were able to remain viable and maintain the 3D structure in vitro. We have proved the concept to use SPIONs as a patterning agent to direct the attachment and self assembly of SPION-loaded endothelial cell spheroids on a prefabricated magnetic template for the formation of 3D cell based structures. A magnetic-directed technique allows quick patterning of cell spheroids in accordance with desirable magnetic patterns, therefore, holding promise for scalable fabrication of complicated 3D multicellular tissue structures. By varying the cell types and the prefabricated magnetic patterns, this magnetic-directed patterning strategy may find use in bioprinting and multicellular tissue graft fabrication. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 1537–1547, 2014.