The risk of recurrence or progression of prior invasive fungal infection, predominantly due to molds, is 11-33% during subsequent stem cell transplantations or myelosuppressive chemotherapy, with a high mortality. Risk factors at the time of transplant include active infection and having received <6 weeks of antifungal therapy, while after transplant prolonged neutropenia and graft-versus-host disease requiring aggressive immunosuppression are important. The use of peripheral blood stem cells has been associated with a lower risk. Minimal data are available regarding the role of preventative strategies such as surgical resection of pulmonary lesions and prophylactic granulocyte transfusions during neutropenia, the optimal duration of antifungal prophylaxis, and the appropriate monitoring strategy. This article critically evaluates these issues and provides recommendations for the secondary prophylaxis of invasive mold infections.