The purpose of this research is to provide a physiological-based Dynamic Difficulty Adaptation (DDA) for rehabilitation of children with Cerebral Palsy (CP). In this paper, we present all the steps of the DDA development by going through (1) the acquisition of physiological signals, (2) the extraction of the physiological signals’ features, (3) the training of a learning classifier of physiological signals' features, and (4) the implementation of the DDA in a game-based rehabilitation system. As a result, we successfully implement a physiological-based DDA based on the user affective state (anxiety and boredom).