Virus-induced gene silencing (VIGS) is a fast and useful method to study gene function. It is based on plant defense mechanisms that interfere with virus gene replication. When a plant gene fragment is used in a VIGS construct, it can elicit co-suppression of the target gene and other paralogs which have sequence similarity, interfering with expression of the plant gene. We have developed a user-friendly tool at the Sol Genomics Network (SGN) to facilitate the design of VIGS constructs for optimal gene suppression taking into account the possibility of silencing only a single gene or multiple members of a gene family. The gene models predicted for tomato and Nicotiana benthamiana genomes can currently be used with the tool. N. benthamiana is the main model plant for VIGS, and has often been used for VIGS experiments with orthologs from other plants species. Using the VIGS tool, the effect of such sequences can be more precisely predicted. The interactive web tool facilitates the prediction of the best regions for silencing, controlling the number of genes to suppress while minimizing off-targets. In the future, gene models from additional Solanaceae species will be added to the tool.