As the population of chronically immunosuppressed individuals continues to grow, the prevalence of fungal infections is increasing. Fungal infections in this patient population represent challenges in diagnosis and management. This article will review the common superficial and invasive mycoses that occur in the solid organ transplant and HIV-infected populations. Disease presentations are reviewed, but emphasis is placed on cutaneous manifestations. Recent advances in antifungal therapy and their direct application to specific diseases provide important new approaches to this complex and often seriously ill patient population.