We studied how linguistic and non-linguistic auditory input is recognized and distinguished by the brain among native and language naïve speakers, and how that might influence the ability to process changes in duration and pitch. 12 Estonian and 12 Russian (with little experience in Estonian) native speakers took part in an MMN experiment using quantity contrast stimuli with changes in pitch and duration. Estonian is a quantity language with a complex and typologically rare three-way contrast while Russian does not exhibit the linguistic quantity category. Two different linguistic stimulus sets (‘SATA’, ‘SAKI’) and one pure tone stimulus set were used. Stimuli differed from each other by the duration of the first vowel [ɑ] (110, 170, 290 ms) and pitch change (level vs falling tone). The sine wave stimulus elicited a more persistent MMN wave with larger amplitude in both language groups, while linguistic stimuli elicited a more pronounced MMN response among the Estonian native speakers. Among the Russian native speakers, the only considerable MMN response for linguistic stimuli was elicited by a clear durational change; while the Estonian native speakers had an MMN response to pitch changes as well. This study is the first ERP study to support previous behavioral findings showing that native Estonian speakers used both durational and pitch cues to discriminate quantities while Russian native speakers used mainly durational cue, while also pointing out some possible limitations and directions for future research.