Recently, electrophysiological measures, especially event-related potentials (ERP), have been increasingly used for investigating the brain mechanisms of music perception. This article aims to briefly review the ERP studies on harmony processing, one of important aspects of music experience, and to identify problems to solve in future research. It has been repeatedly reported that an ERP component termed the early right anterior negativity (ERAN) was elicited in response to chords harmonically inappropriate or incongruent with musical context. However, the nature of cognitive processes reflected in this negativity is still unclear. In addition, similarities and differences between ERAN and the other brain responses, e.g., MMN and N5, obscure the correspondence between these indices and different cognitive processes involved in music perception. The validity of research on harmony processing, and contributions of these studies to the musical therapy domain were also discussed.