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Twenty-four fungal endophytes, isolated from a wild relative of barley, <i>Elymus repens,</i> were screened in barley against an isolate of <i>Fusarium culmorum</i> and an isolate of <i>Pyrenophora teres</i> under controlled conditions. In all experiments, the endophytes were applied individually as seed dressings. Five endophytes could significantly reduce symptoms of <i>Fusarium culmorum</i> (<i>Periconia macrospinosa</i> E1 and E2<i>, Epicoccum nigrum</i> E4, <i>Leptodontidium</i> sp. E7 and <i>Slopeiomyces cylindrosporus</i> E18). In particular, treatment with <i>Periconia macrospinosa</i> E1 significantly reduced <i>Fusarium</i> symptoms on roots by 29–63% in two out of four experiments. Using, a <i>gfp</i> transformed isolate of <i>P. macrospinosa</i> E1, it was possible to show that the fungus was present on roots 14 days after sowing, coinciding with the disease scoring. To test for a potential systemic effect of the seed treatment, eight endophyte isolates were tested against the leaf pathogen <i>Pyrenophora teres.</i> Three isolates could significantly reduce symptoms of <i>P. teres</i> (Lasiosphaeriaceae sp. E10, Lindgomycetaceae sp. E13 and <i>Leptodontidium</i> sp. E16). Seed treatment with Lasiosphaeriaceae sp. E10 reduced net blotch leaf lesion coverage by 89%, in one out of three experiments. In conclusion, specific endophyte isolates exerted varying degrees of protection in the different experiments. Nevertheless, data suggest that endophytic strains from <i>E. repens</i> in a few cases are antagonistic against <i>F. culmorum</i> and <i>P. teres</i>, but otherwise remain neutral when introduced to a barley host in a controlled environment.