The study aimed the evaluation of the effect of osseous repair in the synthetic hydroxyapatite cylinder (HA) implanted in rabbit’s tibia. Fifteen adult animals, weighing around 2.5 and 3.0 Kg, sourced by the Fluminense Federal University Animal Lab were anesthetized with spinal anesthesia, and two perforations were created in right tibia and filled with cylinders (2 x 6 mm) of HA. The animals were killed after 28 days for evaluating the HA cylinder through attenuated total reflection infrared microscopy (ATR-FTIR). The two fragments of tibia with the cylinder were collected and fixed in alcohol 70° prior to dehydration in successive alcohol solutions and then impregnated and embedded in methyl-methacrylate. Not stained neither pasted to lamina, sections of 200 µm thickness were analyzed in a Shimadzu IRPrestige-21 Automatic Infrared Microscope (AIM-8800) with ATR Objective Mirror (ATR-8800M). Prior to implantation, HA cylinder was characterized by X-Ray diffraction (XRD), Attenuated Total Reflection- Infra Red microscopy (ATR-FTIR) and X-Ray Fluorescence (XRF). After the implantation, the spectrum of the ATR-FTIR at the interface to neoformed bone was acquired. The hydroxyapatite synthesized was crystalline and stoichiometric with Ca/P ratio of 1.66, becoming carbonated after 28 days of implantation. We conclude that attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is a useful tool for biomaterial evaluation and able to detect the modification of the chemical HA cylinder pattern occurred probably by ions migration in the biological environment.