Brain responses related to auditory processing show large changes throughout infancy and childhood with some evidence that the two hemispheres might mature at different rates. Differing rates of hemispheric maturation could be linked to the proposed functional specialization of the hemispheres in which the left auditory cortex engages in analysis of precise timing information whereas the right auditory cortex focuses on analysis of sound frequency. Here the auditory change detection process for rapidly presented tone-pairs was examined in a longitudinal sample of infants at the age of 6 and 12 months using EEG. The ERP response related to change detection of a frequency contrast, its estimated source strength in the auditory areas, as well as time-frequency indices showed developmental effects. ERP amplitudes, source strength, spectral power and inter-trial phase locking decreased across age. A differential lateralization pattern emerged between 6 and 12 months as shown by inter-trial phase locking at 2–3 Hz; specifically, a larger developmental change was observed in the right as compared to the left hemisphere. Predictive relationships for the change in source strength from 6 months to 12 months were found. Six-month predictors were source strength and phase locking values at low frequencies. The results show that the infant change detection response in rapidly presented tone pairs is mainly determined by low frequency power and phase-locking with a larger phase-locking response at 6 months predicting greater change at 12 months. The ability of the auditory system to respond systematically across stimuli is suggested as a marker of maturational change that leads to more automatic and fine-tuned cortical responses.