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Despite impressive accomplishments in supportive care over the past decade, infections with a diverse group of microorganisms remain leading causes of morbidity and mortality after hematopoietic stem cell transplantation. The epidemiology of infectious complications has shifted substantially in the past decade with changes in antimicrobial prophylaxis, conditioning regimens, and graft manipulation, such that invasive mould infections and late viral infections are now the overriding concerns. Individual patient risk for infections is predicated on multiple disease-specific, patient-specific, and transplant-related factors but often tracks with the cumulative level of immunosuppression (such as dose of corticosteroids used for the treatment of graft vs host disease [GVHD]). New antivirals and antifungals have entered clinical practice and hold considerable promise for improved outcomes.