The crystal chemistry and crystal structure of gem-quality elbaite from the Pederneira mine, São José da Safira, Minas Gerais, Brazil, were investigated by electron microprobe analysis in wavelength dispersive mode, un-polarized Fourier transform infrared spectroscopy, single-crystal neutron and X-ray diffraction. The average chemical formula of the sample resulted X (Na0.73Ca0.06□0.21) Y (Al1.24Li1.02Fe0.41Mn0.18Mg0.07) Z Al6T Si6O18B (BO3)3V (OH)3W (OH0.46F0.54) and the chemical analysis showed an almost homogeneous distribution of the principal elements over the crystal, with significant amounts of Fe (wt% FeO ~ 3.1) and Mn (wt% MnO ~ 1.3) which substitute YAl. The infrared spectrum over the diagnostic range of fundamental hydroxyl stretching vibrations is characterized by three strong absorption bands at 3,591 (ν1), 3,562 (ν2), and 3,491 (ν3) cm−1, respectively. The neutron structure refinement showed: (a) the presence of boron at the B site only and (b) the absence (at a significant level) of aluminum at the T site, which appears to be fully occupied by silicon. Only one proton site was successfully located. The H bond configuration is described with O3 as “donor” and O5 as “acceptor.” The O3–H bond distance corrected for “riding motion” is 0.9834 Å, and H···O5 = 2.238(7) Å, O3···O5 = 3.152(4) Å and O3–H···O5 = 157.7(5)°. The reasons of the positional disorder at the O1 and O2 sites, observed in both neutron and X-ray refinements, are discussed.