Hydrogen internal combustion engine is considered as a suitable pathway to hydrogen economy before fuel cell technologies become more mature and cost effective. In this study, combustion of hydrogen and compressed natural gas (CNG) in a direct injection single cylinder research engine was investigated. Engine performance parameters such as the power, torque, BMEO and COV of hydrogen DI operation were measured and compared to CNG-DI operation. Stoichiometric combustion of CNG at part load (50 throttle opening) is presented and compared with hydrogen at 0.2 and 0.8 equivalent ratio. The slightly-lean hydrogen (0.8 equivalent ratio) resulted in a better overall performance and emission of the engine.