Invasive fungal diseases are sparse but responsible for a high mortality. During systemic diseases, they are less common than bacterial infection but are probably underdiagnosed. Diagnosis of invasive fungal disease might be difficult: clinical signs may mimic systemic diseases, uninvasive diagnostic tools have not been evaluated in this situation and invasive exploration (histology) is rarely done. Guidelines for invasive fungal disease curative treatment are available but preventive strategies need to be evaluated in the population of patients with systemic diseases.