the epidemiology of bacteremia developing during neutropenia has changed in the past decade, with the re-emergence of gram-negative (gn) bacteria and the development of multidrug resistance (mdr) among gn bacteria. we conducted a case-control study in order to identify factors associated with bacteremia due to multidrug-resistant gram-negative (mdrgn) isolates in hematopoietic stem cell transplant recipients. ten patients with mdrgn bacteremia were compared with 44 patients with gn bacteremia without mdr. bacteremia due to burkholderia or stenotrophomonas sp was excluded from analysis (3 cases), because the possibility of intrinsical resistance. infection due to mdrgn bacteria occurred in 2.9% of 342 hematopoietic stem cell transplant recipients. klebsiella pneumoniae was the most frequent mdrgn (4 isolates), followed by pseudomonas aeruginosa (3 isolates). among non-mdrgn, p. aeruginosa was the most frequent agent (34%), followed by escherichia coli (30%). the development of gn bacteremia during the empirical treatment of febrile neutropenia (breakthrough bacteremia) was associated with mdr (p < 0.001, odds ratio = 32, 95% confidence interval = 5_190) by multivariate analysis. bacteremia due to mdrgn bacteria was associated with a higher death rate by univariate analysis (40 vs 9%; p = 0.03). we were unable to identify risk factors on admission or at the time of the first fever, but the occurrence of breakthrough bacteremia was strongly associated with mdrgn bacteria. an immediate change in the antibiotic regimen in such circumstances may improve the prognosis of these patients.