Medium energy ion scattering using 100 keV H+ ions, has been used to investigate the structure of the (2×1) and (1×1) chemisorbed phases of atomic oxygen on Ru(0 0 0 1), aided by a new automated structural search routine. In both phases the O is found to occupy hcp hollow sites directly above second layer Ru atoms, while in the (1×1)-O surface the oxygen chemisorption induces an expansion of the outermost Ru layer spacing. More subtle subsurface structural modifications, and near-surface lateral and rumpling distortions of the Ru surface in the (2×1) phase were also investigated, but the amplitude of these distortions are not formally significant relative to the estimated precision. A 1.6 ML O coverage (1×1) surface phase showed clear evidence for subsurface oxygen and small changes in Ru subsurface layer spacings.