Recent research on the hydrogenase reactions has sought to probe beyond the information that is provided by X-ray diffraction structures. The major challenge of locating 'transient' hydrogen atoms in species that are potential catalytic intermediates is being addressed, using advanced electron paramagnetic resonance (EPR) techniques and theoretical methods. This article discusses recent progress towards a consensus on the structures of different states of the active site of hydrogenases, the mechanisms of activation and hydrogen cycling.