Fungal infections have increased substantially in patients with acute leukemia as well as in patients receiving allogeneic stem cell transplantations. Most frequently Aspergillus ssp. and Candida ssp. are observed. Despite the recent introduction of new azoles and lipid-based formulations of amphotericin B, there are few randomized, controlled studies on the use of antifungal drugs in patients with proven invasive fungal infections. Conventional Amphotericin B is considered gold standard for the treatment of invasive fungal infections, however is limited by nephrotoxicity and infusion related adverse events. Treatment with azoles, e.g. fluconazole, itraconazole or voriconazole is generally well-tolerated. Fluconazole, however, has no activity against Aspergillus ssp. An additional serious problem is an emerging resistance of non-albicans species to fluconazole. Lipid-formulations of amphotericin B seem to be attractive alternative, but considerably higher medical costs limit broader application of lipid formulations of amphotericin B. The current strategies for the treatment of documented fungal infections as well as the role of new antifungal agents are discussed in this review.