Abstract: Soil salinity has a serious impact on plant growth and agricultural yield. Inoculation of crop plants with fungal endophytes is a cost-effective way to improve salt tolerance. We used metabolomics to study how Trichoderma harzianum T-22 alleviates NaCl-induced stress in a sensitive barley (Hordeum vulgare L.) cultivar (Gairdner) and compared this to the response in a more tolerant cultivar (Vlamingh)GC-MS was used to analyse polar metabolites and LC-MS to analyse lipids in roots during the early stages of interaction with Trichoderma. Inoculation reversed the severe effects of salt on root length in cv. Gairdner and, to a lesser extent, improved root growth in cv. Vlamingh. Biochemical changes showed a similar pattern in inoculated roots after salt treatment. Sugars increase in both cultivars with ribulose, ribose and rhamnose specifically increased by inoculation. Salt stress caused large changes in lipids in roots but inoculation with fungus greatly reduced the extent of these changes. Many of the metabolic changes in inoculated cv. Gairdner after salt treatment mirror the response of uninoculated cv. Vlamingh but there are some metabolites that changed in both cultivars only after fungal inoculation. Further study is required to determine how these metabolic changes are induced by fungal inoculation.