Prion diseases are a group of neurodegenerative disorders characterized by astrocytosis and progressive neuronal degeneration. As a causative agent, prions have been intensely investigated in different experimental models. However, the mechanisms and pathways involved in the prion-induced neurological dysfunction are poorly understood. In this work we have investigated the influence of prion infection on the gene expression profile in a human neuroblastoma cell line. Using a DNA microarray and quantitative reverse transcriptase-polymerase chain reaction methods, we have analysed in SH-SY5Y cells the effects of a synthetic peptide corresponding to the 106-126 neurotoxic region of the cellular human prion protein. Our results show that addition of this peptide to the neuronal culture specifically changes the expression of a relative high number of genes, and causes a progressive neuronal death even in the absence of microglia.