Background: An appropriate regimen in the empirical therapy of neutropenic fever episodes must be individualized at each institution. Hospitals have different patterns of microbial isolates and antibiotic resistance that must be taken into account. The aim of this study was to investigate isolates of bacteremia and their antibiotic susceptibility in patients with hematological malignancies. Methods: All positive blood cultures at a medical center in Taiwan between 1999 and 2002 from patients with hematological malignancies were evaluated. Eleven kinds of antibiotics were tested for antimicrobial activities. The risk factors for mortality were evaluated. Results: Three hundred seventy-one episodes of bacteremia in 266 patients with hematological malignancies were recorded. Gram-negative bacilli (GNB) were still predominant and accounted for 78.2% of isolates, followed by gram-positive cocci for 20.8% of isolates, and anaerobes for 1% of isolates. Escherichia coli was the most common isolated organism accounting for 27.5% of GNB isolates. Other isolates included Klebsiella pneumoniae (19.3%), Pseudomonas aeruginosa (11%), and Enterobacter cloacae (10.1%). The most isolated microorganisms were susceptible to cefoperazone/sulbactam, piperacillin/tazobactam, cefepime or imipenem. Age, GNB microorganism and inadequate empirical antibiotics were risk factors. Conclusions: We suggest that cefoperazone/sulbactam, piperacillin/tazobactam, cefepime or imipenem is an ideal empirical therapy.