Auditory event-related potentials (ERPs) have consistently been used in the investigation of auditory and cognitive processing in the research and clinical laboratories. There is currently no consensus on the choice of appropriate reference for auditory ERPs. The most commonly used references in auditory ERP research are the mathematically linked-mastoids (LM) and average referencing (AVG). Since LM and AVG referencing procedures do not solve the issue of electrically-neutral reference, Reference Electrode Standardization Technique (REST) was developed to create a neutral reference for EEG recordings. The aim of the current research is to compare the influence of the reference on amplitude and latency of auditory mismatch negativity (MMN) as a function of magnitude of frequency deviance across three commonly used electrode montages (16, 32, and 64-channel) using REST, LM, and AVG reference procedures. The current study was designed to determine if the three reference methods capture the variation in amplitude and latency of MMN with the deviance magnitude. We recorded MMN from 12 normal hearing young adults in an auditory oddball paradigm with 1,000 Hz pure tone as standard and 1,030, 1,100, and 1,200 Hz as small, medium and large frequency deviants, respectively. The EEG data recorded to these sounds was re-referenced using REST, LM, and AVG methods across 16-, 32-, and 64-channel EEG electrode montages. Results revealed that while the latency of MMN decreased with increment in frequency of deviant sounds, no effect of frequency deviance was present for amplitude of MMN. There was no effect of referencing procedure on the experimental effect tested. The amplitude of MMN was largest when the ERP was computed using LM referencing and the REST referencing produced the largest amplitude of MMN for 64-channel montage. There was no effect of electrode-montage on AVG referencing induced ERPs. Contrary to our predictions, the results suggest that the auditory MMN elicited as a function of increments in frequency deviance does not depend on the choice of referencing procedure. The results also suggest that auditory ERPs generated using REST referencing is contingent on the electrode arrays more than the AVG referencing.