To reduce the fossil carbon dioxide emissions, net-carbon free fuels are in the focus of research and development of internal combustion engines. Powering an ICE with hydrogen needs to adjust several aspects of the layout and the combustion process control because of the special combustion relevant characteristics. Especially the knock resistance of gaseous fuels, which is described by the Methane Number, has an important impact on irregular and uncontrolled pre-ignition events caused by the global and local thermodynamic state variables. The geometric compression ratio and the engine’s operation point have an essential effect on the maximum temperature and pressure in the cylinder. Also, residual gas, AFR, local hot zones in the cylinder and oil or soot particles may influence knocking. The paper will deal with these issues using analytical analyses and 1d simulation tools whereby the main focus is on cylinder selective compression rations and its consequences for the gas exchange and engine performance. Further, different mixtures of natural gas and hydrogen will be investigated and its effects on knocking, efficiency and IMEP. The investigations are executed at a test engine which is part of a cogeneration unit or also called combined heat and power unit. This test engine has cylinder individual compression ratios of a range from 7 till 13, which are realized by machining the piston and an additional distance plate between cylinder head and engine block.