The aim of this study was to accurately describe the initial processes of flax-root infection by Fusarium oxysporum f.sp. lini. A strain transformed with a GUS gene could be detected by the intense turquoise staining when metabolism was active. The stained fungus was observed on root surfaces in zones where exudation occurred: tips, hairs, rootlets, and wounds. Elsewhere, the mycelium was unstained. The external mycelium penetrated into undifferentiated cells, such as the renewed protodermis cells of the mature root, and the young apical cap cells of the emerging rootlets. The fungus grew and reached the subapical meristem and remained as a permanent internal site of infection. Hyphae grew in and between the undifferentiated cells of the root. When these cells differentiated, the fungus was destroyed in some cells (cortex with endodermis, phloem tubes) but not in others, which became infected cells. The protodermis became the infected cells and hairs of the epidermis. The hyphae did not grow transversely from the epidermis to the stele nor acropetally from apex to the tracheids or vessels. The xylem tissue became infected when it was an undifferentiated group of cells just formed from subapical initials.