Infections in patients with hematopoietic stem cell transplantation (HSCT) continue to remain a formidable challenge for transplanters, caregivers, and patients. The problem has been exacerbated in recent years due to the emergence of multidrug-resistant (MDR) pathogens especially among bacteria. Despite the many obvious developments in diagnostic technology and infection control practices, morbidity, mortality, and cost of care remains high due to infections in the setting of HSCT. Molecular methods in diagnosis of pathogens, improvement in infection prevention and control practices, and better use of antimicrobial therapy and prophylaxis based on pharmacokinetic-pharmacodynamic considerations and immunizations have improved outcome among HSCT patients, but a lot more remains to be achieved. Some unanswered queries persist, for example, the value of surveillance microbiology-based empirical antimicrobial therapy; the absence of decolonization therapy for MDR Gram-negative bacilli; and the role of host microbiome in influencing predilection, course, or outcome in infections. The current chapter provides a summary of the existing literature and attempts to elicit the standard of practice in the management of patients with regard to infections in the HSCT scenario.