Developmental dyslexia has been separately associated with the presence of ectopic collections of neurons in layer I of neocortex (ectopias) and with alterations in processing rapidly changing stimuli. We have used BXSB/MpJ-Yaa mice, some of which have neocortical ectopias, to directly test the hypothesis that ectopias may alter auditory processing. Auditory event related potentials (AERPs) were elicited by pairs of 10.5 kHz tones separated by silence, 0.99 kHz, or 5.6 kHz tones of variable duration. Half of the mice tested had 1-3 ectopias in frontal or parietal cortex, and half had no ectopias. Mice with ectopias showed a reduced response to the second 10.5 kHz stimuli only when it was preceded by short duration 5.6 kHz tones. These results indicate that BXSB mice are an excellent model for determining how focal neocortical anomalies alter sensory processing.