The incidence of invasive fungal infection has increased worldwide along with the increasing population of high risk patients. Recently developed antifungal agents, such as second-generation triazoles and echinocandins, provide the potential to improve therapeutic options against invasive fungal infections. However, treatment of invasive fungal infections has been hampered by both intrinsic and acquired resistance to antifungal agents among many fungal pathogens. A better understanding of the clinical impact of antifungal resistance is important for selecting the proper antifungal agent in patients with systemic fungal infections. This article reviews the current situation with regard to intrinsic and acquired resistance of clinically significant yeasts and filamentous fungi against currently available antifungal agents.