The crystallographic structures of seven refractory metal (Ti, V, Cr, Nb, Mo, Ta and W) disilicides with the C11b, C40 and C54 structures have been refined through analysis of single-crystal X-ray diffraction data. Crystallographic parameters refined are lattice constants, atomic parameters and the space group of the C40 disilicides. In most of previous studies, silicon atoms have been considered to locate at the ideal positions so that the refractory metal atoms are perfectly six-fold coordinated in RSi2 layers prevailing in all the three structures. The present analysis shows that the silicon atoms are displaced from the ideal positions. The magnitude of such displacement is found to be closely related to the interatomic distance in these pseudo-hexagonally arranged RSi2 layers. The space group of three of the four C40 disilicides, VSi2, CrSi2 and TaSi2, is determined to be P6422, which is of chirality with respect to that (P6222) assigned in the previous studies.