Both solid organ and hematopoietic stem cell transplant candidates and recipients are at high risk for healthcare-associated infections due to their underlying diseases, comorbid conditions, as well as the receipt of augmented immunosuppression to prevent rejection. Partnership between transplant physicians, institutional leaders, and infection preventionists allows for the accommodation of this growing vulnerable patient population into institutional risk assessments and hazard analyses. In addition, advancements in diagnostics and molecular typing have provided important information regarding sources of transmission of multidrug-resistant or opportunistic pathogens, thus informing strategies for mitigating risk and controlling outbreaks. Here we review common healthcare-associated infections and strategies for source control, prevention, and curbing outbreaks when detected.