Abstract Background Hematopoietic stem cell transplantation (HSCT) is a potentially curative therapy for an increasing number of neoplastic and hematological diseases. However, these patients are at high risk of acquiring infections due to a complex interaction involving organ dysfunction, tissue damage, pathogen exposure, pathogen virulence, and the overall state of dynamic immunosuppression varying according to different phases of immunologic reconstitution after HSCT, and the need for immunosuppressants to prevent and treat non-infectious complications such as graft-versus-host disease (GVHD). Methods All patients under 16 years old who underwent HSCT at the “Dr. José Eleuterio González” University Hospital, a referral center in Northeast Mexico, from March 2019 to October 2023, were included. Clinical, epidemiological, and analytical characteristics of the patients and infectious episodes during pre-engraftment, early engraftment, and late engraftment periods were analyzed. Results In the studied period, a total of 75 patients underwent HSCT, of whom 52 (69%) experienced infectious events (IEs). A total of 136 IEs were documented, averaging 2.5 IEs per patient. Among these, 40% were viral infections, 33% bacterial, 6.6% fungal, 0.7% parasitic, and 19.3% were indeterminate. The most prevalent baseline diagnoses were acute lymphoblastic leukemia (52%), acute myeloid leukemia (19%), and aplastic anemia (12%). Seventy-two percent of the patients underwent a haploidentical stem cell transplantation, and the graft was sourced from peripheral blood stem cells in 75% of the population. Bacterial infections were predominant in the pre-engraftment period, whereas viral infections were more frequent in early and late engraftment. The distribution of these IEs by period is shown in Figure 1. Among bacterial infections, bloodstream infections (BSIs) accounted for 56%, followed by skin and soft tissue infections (14%) and gastroenteritis (13%). Of the 26 BSI events, 73% were caused by Gram-negative bacilli, including 8 cases of Escherichia coli (42%), 6 cases of Pseudomonas aeruginosa (32%), 2 cases of Klebsiella pneumoniae (11%), and 1 case each of Acinetobacter calcoaceticus, Salmonella enterica and Stenotrophomonas maltophilia (5%). 44% of these exhibited extended-spectrum beta-lactamase (ESBL), and 19% were carbapenem-resistant. The remaining 27% of BSI were caused by Gram-positive cocci: Staphylococcus epidermidis (43%), Streptococcus viridans group (29%), Staphylococcus aureus, and Rothia mulcilaginosa (14% each). 17% of all BSI were central line associated bloodstream infection (CLABSI). Among viral infections, cytomegalovirus (CMV) was the most frequent agent at 46%, followed by SARS-CoV-2 and BK virus at 14% and 11%, respectively. Among the fungal infections, we identified 9 cases of invasive fungal disease (IFD), four cases of possible IFD, two of probable IFD and three cases of proven IFD were identified, including one case each of mucormycosis (zygomycetes), Candida tropicalis fungemia, and Aspergillus niger pneumonia. Additionally, one case of intestinal giardiasis, was identified, accounting for 0.7% of the total. Conclusion Infections represent one of the major adverse events in patients undergoing HSCT. It is essential to understand the local epidemiology in each hospital center to tailor international guidelines to the available resources in each institution, which is crucial in improving strategies for preventing, detecting, and providing timely treatment for these infectious complications and their clinical outcomes. Figure 1. Distribution of infectious events among the post-HSTC periods.