Hydroxyapatite nanorods (HA) were fabricated using caffeine as a modifier at room temperature. Various concentrations of caffeine were utilized to synthesize the HA nanoparticles to analyze its effect on size, shape and morphology. The formation of phosphate ion was confirmed by Fourier Transform spectrophotometer (FTIR). Crystalline structure and phase of the nanoparticles was confirmed by x-ray diffraction study (XRD). The formation of HA nanorods with diversified morphology was confirmed by Transmission Electron Microscope (TEM) images. The results acquired in this study reveals that the HA nanoparticles synthesized using caffeine are uniform and evenly scattered nanorods. The average size of the nanorods obtained from the XRD study was in the range of 20-30 nm. The TEM and SAED investigation revealed the shape, morphology and arrangement of HA nanorods with higher crystallinity. This investigation claims that caffeine is a natural modifier to produce HA nanorods.