The location and orientation of the carbonate ion in the channel (A) and phosphate (B) positions of hydroxyapatite (CHAP) have been investigated by single-crystal X-ray structure and Fourier transform infrared (FTIR) spectroscopy, using crystals synthesized at high pressure. The type A carbonate ion is oriented in the apatite channel with two oxygen atoms close to the c-axis and the B carbonate ion is located near a sloping face of the substituted phosphate tetrahedron. Close comparison of FTIR and X-ray structure results shows that a Na-bearing CHAP containing approximately equal amounts of A and B carbonate ions is a realistic model for the overall crystal structure of biological apatite. However, the absence of distinct OH stretch and OH libration bands indicates that the hydroxyl content of biological apatite is disordered in respect to its orientation and precise location both in the channel and elsewhere in the structure.