Hydroxyapatite (HAP) nanoparticles with uniform morphologies and controllable size were synthesized successfully by molecular template hydrothermal approach. The organic alcohols including ethanol, glycol, glycerol and butanol were used as templates to regulate the nucleation and crystal growth. The synthesized powders were characterized by X-ray diffraction, Fourier infrared spectrum and trans- mission electron microscopy. The results showed that the obtained HAP particles were uniform rod-like crystals, and the template molecular structures had significant effect on the morphology and size of HAP particles. The template molecules with longer hydrophobic groups resulted in longer particle length and larger aspect ratio. Compared with the concentration of template molecules, the template molecular structure showed larger influence on controlling the HAP morphology and size. Furthermore, the for- mation mechanism of these rod-like HAP particles prepared by alkyl alcohol templates was discussed. Moreover, hydrothermal treatment temperature and time could be also used for controlled preparation of HAP nanoparticles.