In this letter, we propose a novel approach for use in the analytical modeling of the overall performance of a Hybrid ARQ (type I and II) together with arbitrary channel model, based on Hidden Markov Model (HMM). Using the combined HMM model developed for involved ARQ protocols with the finite state channel model, such critical performance measure as throughput and delay can be derived in closed form. Analytical results are derived for Stop-and-Wait as well as Go-back-N type together with the type I and type II Hybrid ARQ scheme adopted. We compare the analytical results along with the simulation results in order to check the correctness our model, and show the efficiency of our approach by applying it to realistic environments such as the CDMA IS-95 system with its derived equations.