The recent discovery of a mirror neuron system sets a challenge for a philosophy of experience such as phenomenology, because in humans and monkeys the mirror system seems to transform seen actions into an inner representation of these actions. This paper tries to outline the guidelines of a transcendental-phenomenological analysis of alterity, different from empirical research. The transcendental research must provide a criterion for interpreting the results of empirical science. On this basis the paper compares the phenomenological analysis of alterity with some results of neuroscientific research. It is argued that Edmund Husserl presents an analysis that enables us to avoid misinterpretations of the role and function of the mirror neuron system.