The present study seeks to identify effects of a common genetic polymorphism in the human nicotinic alpha4beta2 receptor on components of the cognitive event-related potentials in auditory and visual modalities. The same sense thymine-to-cytosine polymorphism (c.1629T-C; Ser543Ser) was shown to preferentially modulate early components in both modalities. Specifically, the auditory N1 component amplitude was higher for T allele homozygotes than for C allele carriers. The visual P1 component revealed the same pattern of significant polymorphic modulation, but the later N1 amplitude differences were only marginally significant. There was no reliable indication of interactions between genotype and task factors. Parallel modulation of early latency modality-specific event-related potential (ERP) components in vision and audition may indicate that the CHRNA4 polymorphism affects factors that are common to top-down modulation of sensory processing across modalities.