Can we synthesize artificial composite materials that have a similar nanostructure to bone in vitro? From the viewpoint of self-organization, a novel apatite/collagen nanocomposite was developed. As a result, apatite nanocrystals aligned along collagen molecules, the nanostructure quite similar to bone. The self-organization in the composite concurred at the almost same condition for bone formation. Origin of self-organization was comprehended on the basis of chemical interaction between organic functional groups and surfaces of inorganic crystals.