In prior studies, we have used a conditional linkage between rare deviations in a regular sound pattern to determine if the auditory system can use the first deviation to anticipate the probable features of the second deviation (i.e., make a conditional inference). This study was designed to test two hypotheses about why the mismatch negativity (MMN) to a duration deviant sound seems more susceptible to conditional inference effects. The MMNs to duration and frequency glide deviant sounds were significantly smaller when their occurrence was conditionally linked to the identity of a prior deviant as opposed to when they occurred randomly in a sequence. Results provide support for the learned conditional inference interpretation of reduced MMN size to linked deviants. We discuss alternate explanations and conclude that conditional inference studies could provide insight into the dynamics of probability-based prediction in the auditory system.