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A crystal chemical investigation of a natural specimen of whitlockite, ideally Ca9Mg(PO4)6[PO3(OH)], from Palermo Mine (USA), was achieved by means of a combination of electron microprobe analysis (EMPA) in WDS mode, single-crystal neutron diffraction probe (NDP) and single-crystal X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectroscopy. The crystal-chemical characterization resulted in the empirical formula (Ca8.682Na0.274Sr0.045)Σ9.000(Ca0.034□0.996)Σ1.000(Mg0.533Fe2+0.342Mn2+0.062Al0.046)Σ0.983(P1.006O4)6[PO3(OH0.968F0.032)Σ1.000]. Crystal-structure refinement, in the space group R3c, converged to R1 = 7.12% using 3273 unique reflections from NDP data and to R1 = 2.43% using 2687 unique reflections from XRD data. Unit cell parameters from NDP are a = 10.357(3) Å, c = 37.095(15) Å and V = 3446(2) Å3, and from XRD, the parameters are a = 10.3685(4) Å, c = 37.1444(13) Å and V = 3458.2(3) Å3. NDP results allowed a deeper definition of the hydrogen-bond system and its relation with the structural unit [PO3(OH)]. The FTIR spectrum is very similar to that of synthetic tricalcium phosphate Ca3(PO4)2 and displays minor band shifts due to slightly different P-O bond lengths and to the presence of additional elements in the structure. A comparison between whitlockite, isotypic phases from the largest merrillite group, and its synthetic counterpart Ca3(PO4)2 is provided, based on the XRD/NDP and FTIR results.