Abstract: Tomato plants from four different sites in Colombia were used for the isolation offungal endophytes. In total 51 isolates were obtained from roots and further characterised.Growth on different agar media and classification according to their morphology revealed that 20isolates belong to Fusarium species, whereas 17 isolates were difficult to cultivate. The effect ofthe remaining 14 isolates on growth characteristics of tomato plants was analysed and rootcolonisation ability was controlled by reisolation and by microscopical observation. Thoseisolates not showing obvious endophytic growth or which had negative effects on at least one ofthe growth parameters were omitted. This procedure resulted in the selection of three fungalisolates which could be used as potential biological agents in tomato crops.