The study examines the neurophysiological correlates of confirmation bias in the context of vaccination using fixation-related potentials (FRPs). A methodological approach integrating eye tracking and electroencephalography (EEG) was employed in a laboratory experiment, enabling the synchronization of eye movement data with the brain's bioelectrical activity. Participants read texts about vaccination containing positive, negative, and neutral statements, while their reactions were recorded under conditions of congruence and incongruence between the valence of the text and the implicit component of their attitude, measured via the Implicit Association Test. The findings revealed significant differences in neurophysiological responses, including increased potential amplitudes in incongruent conditions for the P200, P300, N350, and N400 components. These responses indicate the activation of selective attention and enhanced perceptual stimulus processing (P200), reallocation of attentional resources and the emergence of cognitive dissonance (P300), emotional categorization (N350), and semantic, including valence-related, mismatch processing (N400). The results underscore the high sensitivity of FRP methods to the cognitive and emotional aspects of information perception. The proposed methodological approach enhances the ecological validity of the study, offering promising opportunities for investigating implicit cognitive processes in naturalistic text perception settings. © 2025 Elsevier B.V., All rights reserved.