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Background: In developing countries, knowledge of antimicrobial resistance patterns is essential to define empirical therapy., Methodology: All the surgery and intensive care wards of two hospitals in Antananarivo were included to study the antimicrobial susceptibility of the pathogenic bacteria causing nosocomial infections. A repeated cross-sectional survey was conducted between September 2006 and March 2008, one day per week. Isolates were identified using classical methods, and resistance to antibiotics was assessed according to the recommendations of the Antibiogram Committee of the French Microbiology Society., Results: Clinical specimens from 706 from 651 patients were collected. Of the 533 bacterial pathogens, 46.7% were Enterobacteriaceae, 19.3% were Staphylococcus aureus, and 19.1% were pathogens from the hospital environment (Pseudomonas aeruginosa and Acinetobacter baumannii).Frequencies of resistance were high, particularly in Enterobacteriaceae; however, the rate of Staphylococcus aureus isolates resistant to oxacillin (13.6 %) was moderate and all these isolates were susceptible to glycopeptids. The percentages of isolates susceptible to ceftazidim were 81.8% for E. coli, 60.9% for Klebsiella, and 52.5% for Enterobacter spp. Resistance to third-generation cephalosporins was due to extended spectrum betalactamases (ESBL). Multivariate analysis showed that diabetes (adjusted OR: 3.9) and use of an invasive procedures (adjusted OR: 3.5) were independent risk factors for resistance to third-generation cephalosporins., Conclusion: A nationwide surveillance programme is needed to monitor the microbial trends and antimicrobial resistance in Madagascar.