Z-contrast imaging, electron diffraction, atom-probe tomography (APT) and density functional theory calculations were used to study the crystal structure of the Mo₃Si phase which was previously reported to have an A15 crystal structure. The results showed that Mo₃Si has an incommensurate crystal structure with a non-cubic unit cell. The small off-stoichiometry in composition of the sample which was revealed by APT and atomic resolutionZ-contrast imaging suggested that site substitution caused the development of split atomic positions, disorder and vacancies.