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The prevalence of invasive fungal infections has increased significantly during organ transplantation, cancer chemotherapy and allogeneic bone marrow transplantation. However, only a limited number of antifungal agents are currently available for the treatment of life-threatening fungal infections. Although new antifungal agents have been introduced in the market, the development of resistance to antifungal drugs has become increasingly apparent, especially in patients with long term treatment. Microbial natural products have always been an alternative natural source for the isolation of novel molecules for various therapeutic applications. Endophytes are the microorganisms that colonize internal tissues of all plant species and represent an abundant and dependable source of bioactive and chemically novel compounds with potential for exploitation in a wide variety of medical, agricultural and industrial arenas. In the present review several metabolites obtained from endophytic fungi with a potential as antifungal agents are mentioned with bioactivity including volatile organic compounds. The compounds reported here with a diverse scaffold can be a potential starting point for new antifungal agents either as such or after chemical modification.