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Empiric antimicrobial coverage in compromised hosts commonly includes pseudomonal coverage but often lacks coverage against Stenotrophomonas maltophilia. Identification of risk factors specific for S. maltophilia infection may lead to prompt initiation of appropriate antibiotics and improved outcome.We conducted a retrospective analysis of pediatric patients with bacteremia due to S. maltophilia or Pseudomonas aeruginosa from April 2002 to July 2014 at a tertiary children's hospital. Patient demographics, underlying disease, clinical course, and treatment were compared between S. maltophilia and P. aeruginosa cases.Nineteen children with S. maltophilia bacteremia and 49 children with P. aeruginosa bacteremia were identified. On multivariate logistic regression analysis, use of carbapenems within 7 days prior to onset (OR, 5.00; 95%CI: 1.25–20.07; P = 0.02) and previous intensive care unit stay (OR, 3.75; 95%CI: 1.13–12.47; P = 0.03) were significantly associated with S. maltophilia bacteremia compared with P. aeruginosa bacteremia. The majority of the S. maltophilia bacteremia patients had central line-associated bloodstream infection (79%), compared with the P. aeruginosa bacteremia patients (37%, P = 0.002). There were nine children (47%) who had polymicrobial infection in the S. maltophilia bacteremia group, in contrast to four (8%) in the P. aeruginosa bacteremia group (OR, 10.13; 95%CI: 2.59–39.56; P = 0.001). Consultation with an infectious diseases physician was associated with a lower rate of persistent S. maltophilia bacteremia (P = 0.04).Stenotrophomonas maltophilia should be considered in breakthrough bacteremia in pediatric patients who receive carbapenems within 7 days prior to onset.