Infectious complications constitute a major cause of morbidity and mortality in pediatric and adult patients undergoing hematopoietic SCT (HSCT). Current guidelines and recommendations for prevention of infections in children after HSCT are presented in this mini review. The paper is based on evidence-based recommendations rated by the strength of the recommendation and the quality of the supporting evidence. Prophylaxis strategy based on risk stratification includes: (1) general infection control in hospital environment, (2) pharmacological approach related to antibacterial, antifungal and antiviral agents and (3) vaccination. Although most studies were carried out on adults only, some included both pediatric and adult patients. No differences in prophylaxis strategy and efficacy among age groups are reported. With changing practices, transplant teams are encouraged to review local patterns of prophylaxis strategy.