We have used electron microscopy and diffraction to refine the structure and investigate the microstructure of Ba(3)Ti(2)RuO(9). The parent compound is hexagonal BaTiO(3) with the space group P6(3)/mmc. Using convergent-beam electron diffraction (CBED) combined with electron-sensitive image plates we have found that the space group of Ba(3)Ti(2)RuO(9) is the non-centrosymmetric group P6(3)mc at room temperature and at approximately 110 K. This is consistent with the Ru and Ti atoms occupying alternate face-sharing octahedral sites in the 0001 direction. This maintains the c-glide, but breaks the mirror normal to the c axis and consequently removes the centre of symmetry. Using powder X-ray diffraction, we have measured the lattice parameters from polycrystalline samples to be a = 5.7056 +/- 0.0005, c = 14.0093 +/- 0.0015 A at room temperature. Using high-resolution electron microscopy (HREM) we observed highly coherent, low-strain {10\bar 10} grain boundaries intersecting at 60 and 120 degrees . From CBED we deduce that adjacent grains are identical but for the relative phase of the Ti and Ru atom ordering along the c axis. HREM also revealed occasional stacking faults, normal to the c-axis.