To investigate the effects of cell–cell interactions on cellular function, the microenvironment surrounding cells should be precisely controlled. Here, we describe a cell patterning technique, which utilizes magnetic force and magnetite nanoparticles. This method was used to develop cell culture arrays for investigation of cell behaviors in angiogenesis. Pin holder devices that contain more than 6,000 pillars on the surface are used for fabricating the cell culture arrays by setting it on a magnet. The magnetically labeled cells were arranged by magnetic distribution. When the human umbilical vein endothelial cells are arranged at 250 µm intervals (5.9 cells/spot), the cells spread toward other cell cluster on adjacent spots in 4.5 h, and formed cord-like structures in 8.5 h. It was shown that cell–cell interactions were successfully investigated using magnetic cell arrangement. Biotechnol. Bioeng. 2009; 102: 882–890. © 2008 Wiley Periodicals, Inc.