The evolution of the flora and its resistance to different antimicrobials in neutropenic patients submitted to high-dose chemotherapy with autologous blood stem-cell transplantation, and the relation of these findings to the etiology of the infections the patients developed was studied in order to evaluate the suitability of the chemoprophylaxis and the empirical antibiotic therapy used. Forty-one patients were analyzed in a period of 28 months. The chemoprophylaxis used was levofloxacin, fluconazole and acyclovir. The empirical sequential treatment was an initial administration of cefepime, followed by teicoplanin and amikacin. Cultures were done of nasal and pharyngeal smears, Hickman catheter and stools, 1 day before chemoprophylaxis started and then on days 5 and 9. In the case of fever, three sets of blood cultures and urine cultures were done and samples from areas related to the clinical condition were analyzed. Levofloxacin induced the selection of resistant strains or species in the flora and in the infectious agents. Fluconazole also selected resistant species in the flora. Seventeen infections were documented in eleven patients, produced by Gram-positive bacteria in thirteen cases (81.25%) and by Gram-negative bacteria in three (18.75%). The coagulase negative staphylococci and Enterococcus faecalis were the most frequent agents of infection. We identified on nine occasions the same microorganism in the flora and in the pathological product; this suggests its endogenous origin and supports the use of prospective cultures of the flora, monitoring the sensibility of the microorganisms isolated to the antimicrobials used in chemoprophylaxis and empirical treatment.