We examined the neural correlates associated with a short gap between two identical pure tones (within-channel) and between two different tones (between-channel) in an odd-ball paradigm. Gap durations were selected such that a gap between identical tones was as discriminable as a gap between two different tones. Spatio-temporal dipole source modeling of electrophysiological data revealed a significant difference between standard and deviant gap stimuli, with mismatch negativity responses that were comparable in amplitude and latency for within- and between-channel conditions. Therefore, the ability to automatically register discontinuity (i.e., gap) within and between channels is comparable despite significant differences in gap size. The dipole source modeling suggests that both within- and between-gap signals are represented in or near the primary auditory cortex.