Plants have developed defense mechanisms against viruses by using an RNA silencing-based process, which has many common features with the endogenous RNA silencing pathway used for regulating the level of transcripts derived from developmental genes. In the virus-induced gene silencing (VIGS) method, it is possible to take advantage of this mechanism by inserting a plant nucleic fragment within the viral genome to knock down the corresponding gene. This tool has been used in many species as a fast and easy reverse genetics technique in order to gain information on the role of genes with poorly understood functions. Here we describe in detail two Agrobacterium-mediated infection protocols in flax, based on a whole plant vacuum infiltration and a leaf syringe infiltration that systemically impact the transcript levels in the stem.