Over the past three decades, autologous and allogeneic haematopoietic stem cell transplants (HSCTs) have become effective treatments for a variety of malignant and nonmalignant conditions. Patients who undergo HSCT receive high doses of chemotherapy and/or radiation that induce a prolonged period of profound immunodeficiency, placing them at high risk for infection from a panoply of opportunistic organisms. Although supportive treatment for these patients has markedly improved, 10-20% of allogeneic HSCT recipients will ultimately succumb to infection. Joint guidelines to prevent opportunistic infection were released in 2000 by the Centers for Disease Control, the Infectious Diseases Society of America, and the American Society of Blood and Marrow Transplantation; however, treatment decisions for these patients are often based on limited studies or depend on institution-specific transplant protocols and antibiotic resistance patterns. This paper will discuss new agents for preventing bacterial, fungal and viral infections in HSCT recipients.