This paper presents highly resolved large eddy simulations (LES) of an internal combustion engine (ICE) using an immersed boundary method (IBM), which can describe moving and stationary boundaries in a simple and efficient manner. In this novel approach, the motion of the valves and the piston is modeled by Lagrangian particles, whilst the stationary parts of the engine are described by a computationally efficient IBM. The proposed mesh-free technique of boundary representation is simple for parallelization and suitable for high performance computing (HPC). To demonstrate the method, LES results are presented for the flow and the combustion in an internal combustion engine. The Favre-filtered Navier-Stokes equations are solved for a compressible flow employing a finite volume method on Cartesian grids. Non-reflecting boundary conditions are applied at the intake and the exhaust ports. Combustion is described using a flame surface density (FSD) model with an algebraic reaction rate closure. A simplified engine with a fixed axisymmetric valve (see Appendix A) is employed to show the correctness of the method while avoiding the uncertainties which may be induced by the complex engine geometry. Three test-cases using a real engine geometry are investigated on different grids to evaluate the impact of the cell size and the filter width. The simulation results are compared against the experimental data. A good overall agreement was found between the measurements and the simulation data. The presented method has particular advantages in the efficient generation of the grid, high resolution and low numerical dissipation throughout the domain and an excellent suitability for massively parallel simulations.