A pathogenic strain of Fusarium oxysporum f. sp. lycopersici transformed with the glucuronidase (GUS) reporter gene was used to study the colonization process of tomato (Lycopersicon esculentum) roots in hydroponic culture. The plants were treated exactly as those used in a different study with a non-pathogenic strain of F. oxysporum in order to compare the two types of colonization process. The pathogenic strain rapidly colonized the root surface, forming a dense network of hyphae – shown by the GUS staining assay – as early as 48 h after inoculation. The first images of the pathogen penetrating into the epidermis of the root were observed 24 h after inoculation. The plant showed defence reactions mainly in the hypodermis, but also in the cortex. Generally these barriers failed to prevent the centripetal growth of the pathogen towards the stele. The GUS activity moved with the actively growing hyphae into the tissues; the stele appeared intensely stained 7 d after inoculation, whereas by this time the hyphae at the root surface did not show any more staining. The hyphae formed a dense network at the apex of the root, but direct contact between hyphae and living cells was prevented by several layers of sloughed cap cells. Although rarely observed, penetration of the pathogen into the apex was possible and led to a rapid destruction of apical cells. The only differences between this pattern of root colonization and that observed for a non-pathogenic strain of F. oxysporum appear to concern the frequency of dead apices and the intensity of fungal colonization in the cortex. When the pathogen passed around the barrier formed in the hypodermis it always reached the xylem, although this barrier and other defence reactions induced at different levels in the cortex always prevented the non-pathogenic strain from reaching the stele. These observations suggest that the main differences between the two types of interaction – between the plant and either the pathogenic or the non-pathogenic strain – are quantitative rather than qualitative.