Defining the molecular toxicity of viral vectors that are or will be in use for clinical trials is a prerequisite for their safe application in humans. DNA chips allow high-throughput evaluation of the profile of transduced cells and have contributed to underlining specific aspects of vector toxicity both in in vitro and in vivo assets. With gene chips we have been able to identify vector-specific properties, such as the cell cycle alteration induced by vector genomic DNA, along with the activation of specific innate immune pathways that can be ascribed to viral particles. We herein describe a detailed protocol for the use of gene chips to dissect the toxicogenomic signature of human and canine helper-dependent adenoviral vectors. We suggest specific procedures suited for the study of these viral vectors, but we also give indications that can be applied to different experimental contexts. In addition, we discuss the in silico elaboration of gene chip raw data which is a crucial step to extrapolate biological information from gene chip studies.