The mismatch negativity (MMN; and its magnetic counterpart, MMNm) is widely used to assess early-stage auditory cortical function in humans and its impairment in various neuropsychiatric disorders. To establish MMN as a useful clinical tool for objective monitoring of auditory cortical function in an individual, we investigated the effect of gender and personality traits on individual difference in MMNm in healthy subjects. Participants were 88 healthy adults (31 women and 57 men). The MMNm in response to the duration or frequency change of tones and those in response to across-phoneme change between vowels /a/ and /o/ were recorded using 204-channel whole-head magnetoencephalography. The temperament and character inventory (TCI) was used to assess individual personality traits. Women were associated with significantly delayed peak latency of phonetic MMNm for the right hemisphere compared with men. Men had greater strength of tonal duration MMNm for the left hemisphere than women. Additionally, the persistence score predicted the strength of phonetic MMNm for the left hemisphere in the combined sample and the tonal duration MMNm for the left hemisphere in men; reward dependence predicted the latency of the tonal duration MMNm for the left hemisphere in men; and cooperativeness predicted the strength of the tonal frequency MMNm for the right hemisphere in women. These results suggest that gender and personality traits have an effect on individual variability of the MMNm. Our observation may provide useful information to establish MMN/MMNm as a clinical tool for monitoring auditory cortical function on an individual basis.