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Many invasive fungal diseases have no characteristic signs or symptoms, and may give negative blood cultures; therefore, clinician may decide to start empirical antifungal therapy particularly in high risk patient (e.g., hematopoietic stem cell transplant, solid organ transplant, and AIDS patients). This increases the incidence of appearance of resistant fungal strains to antifungal drugs. Traditional methods for diagnosis such as wet mount examination and microbiological cultures remain the gold standard methods for fungal disease diagnosis. However, they are time-consuming, insensitive, and have a limited impact on clinical decision-making. Significant progress has recently achieved in diagnostic tools of fungal disease. Antigen and antibody based assays, molecular techniques, and MALDI TOF spectrometry technique and nanotechnology offer more rapid, sensitive and accurate results.