Fuel cells have succeeded in finding their way onto the market. Automotive, portable and combined heat and power applications are commercially available. Still, one major drawback of fuel cells can be found in the use of expensive materials, especially precious metal catalysts. However, the development of new catalyst materials has turned out to be a challenging task because the electrochemical reactions at the electrodes depend on numerous, interdependent parameters. That is why statistical approaches, so-called high-throughput or combinatorial methods, in material processing as well as material characterization have been established. They allow the manufacturing and validation of material libraries which exhibit a wide variety of material parameters, e. g. in the range of morphology or content of certain metal alloys. In this way, development times can be reduced significantly. In addition, micro fuel cells can also be interesting for material development. The small size is advantageous when it comes to material usage, temperature distribution and characterization times. Thus, the combination of combinatorial methods and micro fuel cells can boost material development in fuel cells to a new level. That is why the Fuel Cell Research Center (ZBT) in Duisburg and the Chair for MEMS materials at the Ruhr University of Bochum have merged their competences and developed a new method for the manufacturing and characterization of innovative micro fuel cell libraries. State-of-the-art technologies such as sputter deposition and infrared-thermography are used to generate silicon-based micro fuel cells with changing material properties and to validate them insitu while the fuel cell reaction takes place. Besides a successful proof of concept in a MERCUR-funded research project a first application of the method will be developed in the field of alkaline fuel cells where catalyst and electrolyte materials are lagging behind acid-based fuel cell systems.