The understanding of the basic principles of hydrogen production and utilization by the enzyme hydrogenase is a goal of major importance both for basic research and possible applications in our society. Hydrogenases are enzymes that facilitate the uptake and release of molecular hydrogen using a heterolytic reaction mechanism: H2⇌H++H−⇌2H++2e−. The acidity of H2, which is extremely low, is dramatically increased by binding to a metal. Many of the currently used catalysts for anthropogenic utilization of hydrogen involve precious metals such as platinum, while Nature's catalysts are based on cheap and abundant first row transition metals. Three phylogenetically distinct classes of hydrogenase are known; these are the [NiFe], the [FeFe] and the [Fe] hydrogenases. The first two classes have active sites containing binuclear metal cores with an unusual ligand sphere, whereas the third class harbors a mononuclear iron next to a special organic cofactor. In all these hydrogenases, the protein plays an important role for tuning the active site properties, but also by providing pathways for protons, electrons as well as dihydrogen. An important feature of the native systems is the very high turnover frequency (up to ∼104 s−1). Hydrogenases from (hyper)thermophilic organisms show a remarkable stability at high temperatures (up to ∼100°C) and several [NiFe] hydrogenases (e.g. from Knallgas bacteria) are active even in the presence of ambient levels of molecular oxygen. As discussed in this chapter, a combination of X-ray crystallography, spectroscopy, electrochemistry and quantum chemistry was instrumental in characterizing the hydrogenases with respect to their structure and function. Furthermore, mechanisms for the enzymatic reactions are proposed and guidelines for the construction of biomimetic hydrogenase model systems are provided.