Uranium in apatite has been used extensively in geochronologic and petrogenetic studies for over half a century. Because of its high affinity for U and other radionuclides and its thermal annealing behavior, there is also great interest in apatite as a solid nuclear-waste form and an engineered contaminant barrier. Fundamental to our understanding of uranium retention and release by apatite are crystal chemical parameters such as site occupancy, oxidation state, and structural distortions created by this substituent. Despite the interest in U in apatite, the basic crystal chemistry of its substitution in the structure is still unknown. We present the first direct evidence of the site of incorporation and the response of the structure to U(VI). X-ray absorption spectroscopy was used to determine the local structure of U(VI) within synthetic fluorapatite at a concentration of 2.3 wt.%. Extended X-ray absorption fine structure results indicates that U(VI) substitutes into the Ca1 site. To accommodate this substitution the apatite structure significantly distorts such that the Ca1 site approximates octahedral coordination, with 6 uniform U-O distances of 2.06 Å. An unusual X-ray adsorption edge structure, with two inflection points separated by 8.4 eV, and optical emission spectra indicate uranium 6d orbital crystal field splitting. These results indicate that significant amounts of U(VI) can be accommodated in the apatite structure but with an unexpected coordination, which may bear on the ultimate development of apatite-hosted nuclear-waste forms.