The relationship between molecular and crystal structures of organometallic complexes showing intramolecular interactions of the M-H ... H-X type (M = transition metal, X = O, N, and S) has been investigated by a combined use of molecular orbital calculations and crystal packing analysis. Molecular and crystal structures determined by neutron and/or X-ray diffraction data of coordination complexes and clusters showing intramolecular (M-H ... H-X) interactions within the range 1.5-2.5 Angstrom have been retrieved from the Cambridge Structural Database. DFT calculations were performed for the majority of compounds in order to determine the nature of the H ... H interaction. The optimized geometries obtained by DFT are usually in good agreement with the experimentally determined ones, short H ... H distances being also found. Most of the systems analysed, such as cis-[IrH(OHXPMe3)(4)][PF6], involve cationic complexes. It has been found that the counter ion exerts a strong influence in bringing together the two hydrogens. When it is included in the calculations, the agreement between the observed and the calculated structures is much better.