Apatite cement (AC) is a breakthrough in biomaterials for the reconstruction of the bone defect. However, the replacement of AC to bone up to the present time is still controversial for researchers. Several researchers have reported that AC was replaced by bone while others claimed replacement was limited. The aim of this study is to investigate the transformation mechanism of AC to B-Type carbonate apatite (CO3Ap) using different atmosphere. An in vitro study mimicking the body environment was employed in order to examine the effect of setting atmosphere on the composition of set AC. An equimolar of tetracalcium phosphate (TTCP; Ca4 (PO4)2O) and dicalcium phosphate anhydrous (DCPA; CaHPO4) mixed with distilled water was enabled to harden at 37°C and 100% of relative humidity under presence of 5% CO2, 100% CO2, and 100% N2 atmospheres. XRD and FT-IR analyses revealed that in the presence of 100% CO2 and 5% CO2, Btype CO3Ap could be determined and only small amounts of TTCP remained unreacted. On the contrary, in the presence of 100% N2, the CO3-2 bands could not be detected and larger amount of TTCP remained unreacted compared to 5% CO2 and 100% CO2 atmospheres. SEM morphology showed that the microstructure of AC was entangled and locked to each other. In addition, the small needle like crystals appeared in the surface of 100% N2, similar to hydroxyapatite. We concluded that the CO3 -2 ions incorporated in AC during setting reaction may be one of the essential factors for CO3Ap formation.