Hydroxyapatite materials are potentially useful for biomedical application, especially as vehicles for functional molecules. Structural control of bulk apatite materials, such as in the fabrication of hollow microspheres or porous structures, has been studied for this purpose. However, control of the internal structure of the source apatite crystal itself is still a challenge. Here, we show that small organic molecules incorporated in apatite crystals act as porogens which control the porous structure of apatite single crystal. The presence of amino acid under apatite synthesis conditions leads to firm bindings and encapsulation of the amino acid in apatite single crystals. Amino acid elimination by heating or electron beam irradiation enhances the pore formation in apatite single crystal. Moreover, incorporation of an acidic amino acid in apatite induces peapod like nanotubes in apatite single crystals. This study suggests the potential of using small organics for nano-structural control of apatite single crystals which would be valuable for enhancing drug loadings or modulating material digestion in vivo. (c) 2011 Elsevier B.V. All rights reserved.