Virus infections in grapevine develop as compatible interactions, in which the pathogens spread through all plant tissues without inducing a resistance response but affecting morphology of leaves, vegetative growth and productivity. Also, organoleptic properties, acidity and concentration of sugar in the fruit are affected by the viral infections influencing the quality of the must produced from these infected plants. To investigate the global effect of virus infections in grapevine, we compared the transcriptional profiles of virus free and GLRaV-3 naturally infected 'Cabernet Sauvignon' plants. The Affymetrix GeneChip Vitis genome array, version 1.0, was used for the analysis of leaves and berries at two maturation stages: veraison (EL-35) and maturation (EL-38). Infection was confirmed by RT-PCR and also by electronic microscopy that allowed us to observe virus particles in the leaves and berries of the infected plants. A wide spectrum of biological functions was affected by viral infections in all tissues studied. The most relevant changes in gene expression in leaves were associated with synthesis and destination of proteins, transport and metabolism. Also developmental processes, senescence and cell defence were affected. In the fruit, the virus infection affects the maturation process since a reduced number of genes change their expression between veraison and maturation stages in the infected plants compared with healthy plants. Besides, an important number of genes that appear down regulated in the infected fruits at the maturation stage are associated with the processes of biosynthesis of primary and secondary metabolites, metabolism, developmental process, senescence and cell defence. Therefore the maturation process appears incomplete in the infected plants.