Human peroxiredoxin (Prx) play important roles in eliminating hydrogen peroxide generated during cellular mechanisms using electrons from thioredoxin (Trx). Oxidative stress induced by reactive oxygen species (ROS) such as hydrogen peroxide has been implicated in the pathogenesis of several neurodegenerative diseases. We applied the proteomic approach to study protein levels of three subtypes of human Prx in brain regions from patients with Alzheimer's disease (AD) and Down Syndrome (DS). Protein levels of Prx-I and Prx-II were significantly increased in AD and DS. Protein levels of Prx-III, a mitochondrial protein, however, were significantly decreased. We conclude that increased protein levels of Prx-I and Prx-II could provide protection against neuronal cell death induced by hydrogen peroxide. Decreased protein levels of Prx-III could be caused by mitochondrial damage shown in AD and DS. Showing upregulated Prx protein levels provides evidence for the involvement of ROS in the pathogenesis of AD and DS.