Transcription factor AP-2beta may influence brain monoaminergic systems by regulating target genes. Several monoaminergic genes, including the serotonin transporter gene, have AP-2beta binding sites. Late auditory-evoked potentials (P1, N1/P2) and impulsiveness-related personality traits are correlated, and both are modulated by monoaminergic neurotransmission. The present study assesses the impact of two AP-2beta polymorphisms (VNTRs within intron 1 and 2) together with the serotonin transporter polymorphism 5-HTTLPR on late auditory-evoked potentials and personality for the first time. EEG was recorded from 91 male subjects at central electrode positions while tones of six intensity levels were presented. Additionally, subjects completed personality questionnaires. Both AP-2beta polymorphisms revealed significant main effects on P1, and haplotype analysis confirmed the contribution of both AP-2beta-polymorphisms. Additionally, AP-2beta and 5-HTTLPR showed interactions with respect to P1. 5-HTTLPR revealed a main effect on N1/P2 but not P1. Impulsiveness showed an association with intron 1 VNTR. The results are discussed with respect to differential impact of AP-2beta polymorphisms and 5-HTTLPR on the monoaminergic systems. The findings promote replication in a larger sample and suggest a potential usefulness of AP-2beta polymorphisms in explaining or predicting central nervous diseases, drug effects and side effects.