The free piston internal combustion engine used in conjunction with a linear alternator offers an interesting choice for use in hybrid vehicles. The linear motion of the pistons is directly converted to electricity by the alternator, and the result is a compact and efficient energy converter that has only one moving part. The movement of the pistons is not prescribed by a crank mechanism, but is the result of the equilibrium of forces acting on the pistons, and the engine will act like a mass-spring system. This feature is one of the most prominent advantages of the FPE (Free Piston Engine), as the lack of mechanical linkage gives means of varying the compression ratio in simple manners, without changing the hardware of the engine. By varying the compression ratio, it is also it possible to run on a multitude of different fuels and to use HCCI (Homogeneous Charge Compression Ignition) combustion. Furthermore, the reduction of the number of moving parts will decrease engine friction and thus increase efficiency.In this paper, BOOST and SENKIN have been used to investigate engine performance for different fuels. A dynamic model of the complete free piston engine was created that predicts the piston motion and frequency. The gas exchange was simulated with the commercial 1-D code BOOST, which solves the gas dynamic equations. The high-pressure cycle of the commercial 1-D code BOOST was replaced by detailed chemistry calculations in the SENKIN code. For combustion reduced mechanisms of Diesel (n-heptane and toluene), gasoline (iso-octane, toluene and n-heptane), natural gas (methane, ethane, propane and n-butane) and hydrogen have been used. All mechanisms consisted of about 60-100 species. The results show that a decreased cetane number requires higher compression ratios in order to position the ignition properly. The higher compression ratios give an increase in engine speed, power and efficiency.