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The focus of this paper is to compare results from 3D combustion simulations when using either a single-step or a two-step description of the chemistry of combustion in a two stroke free piston diesel engine. To reduce the computational cost, only one sector of the whole cylinder is computed, i.e. one fuel spray. The simulation starts after the exhaust ports are closed and ends before the exhaust ports opening. The fuel injection is described by a Lagrangian method where the break up and interaction of the droplets are taken into account as well as droplet wall interaction and evaporation. Turbulence is modeled using the standard high Reynolds number k-ε model. The combustion of fuel vapor is modeled by the the Eddy Dissipation Combustion Model (EDCM). In the case of two-step chemistry, the combustion of CO is taken into account. The kinetic rate of CO combustion is determined from a global expression.