The simulation of combustion chemistry in internal combustion engines is challenging due to the need to include detailed reaction mechanisms to describe the engine physics. Computational times needed for coupling full chemistry to CFD simulations are still too computationally demanding, even when distributed computer systems are exploited. For these reasons the present paper proposes a time scale separation approach for the integration of the chemistry differential equations and applies it in an engine CFD code. The time scale separation is achieved through the estimation of a characteristic time for each of the species and the introduction of a sampling timestep, wherein the chemistry is subcycled during the overall integration. This allows explicit integration of the system to be carried out, and the step size is governed by tolerance requirements. During the subcycles each of the species is only integrated up to its own characteristic timescale, thus reducing the computational effort needed by the solver. The present ODE solver was first validated using constant pressure batch reactor simulations with two different reaction mechanisms. Then the solver was coupled with the KIVA-4 code, and validated using HCCI and DI diesel combustion cases. Performance is compared with the commonly used DVODE chemistry solver and the results show that significant reductions in the total computational time with comparable accuracy are obtained with the new solution methodology.