Abstract: Fungal endophytes live naturally inside plants without causing symptoms. On the contrary, they can promote plant growth and increase tolerance to abiotic and biotic stress. Clonostachys rosea isolate IK726 efficiently controls seed- and soil-borne diseases and can furthermore promote plant growth, but its ability to colonise plants internally is unknown. The present work evaluated the influence of root inoculation on endophytic colonisation of tomato by IK726. Growth of C. rosea was identified from plants inoculated by root dipping or by soil drenching. Sections from 0 to 5 cm from the stem basis were sampled and surface disinfected. The earliest time point for stem isolation of C. rosea was 11 days after inoculation while the latest time point was 39 days after inoculation. In contrast to the stem sections, surface disinfection of roots eradicated all culturable fungi. Therefore, root pieces were washed only in water which resulted in growth of C. rosea from more than 50% of the pieces, irrespective of the inoculation method. Pre-inoculation of roots with C. rosea reduced the development of the tomato wilt pathogen Fusarium oxysporum f.sp. lycopersici. However, it was not possible to determine if the effects were related to endophytic colonisation by C. rosea. In conclusion, we have shown for the first time that C. rosea can live as an endophyte in tomato stems and our results suggest that the endophytic colonisation is systemic, with the fungus growing from the roots and into the stem.