A discrete time-domain based system identification method for PWM DC-DC converters is presented. The proposed procedure is capable of successfully reconstructing the system's model from an arbitrary excitation at the command input. In this study, a step perturbation was applied, which is simple to apply and has an intuitive interpretation of the output response. The effects of switching and quantization noise were overcome by choosing the sampling instance to be after the switching oscillations decay significantly and by averaging the responses of synchronously perturbed sequences. The proposed method was evaluated on Buck and Boost converters. The digital data acquisition procedure was implemented on a TMS320F2407 DSP core. Excellent agreement was found between simulations and experimental results.