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Neonatal sepsis, a life-threatening condition, presents with non-specific clinical manifestations and needs immediate empirical antimicrobial therapy. Choosing an appropriate antibiotic regimen covering the most probable pathogens is an important issue. In this study we compared the effectiveness of ceftizoxime and amikacin in the treatment of neonatal sepsis both in combination with ampicillin. In a randomized clinical trial, all term neonates with suspected sepsis referred to Bahrami hospital during March 2008 to March 2010 were evaluated. Patients were randomly recruited into two groups; one group receiving ampicillin and amikacin and the other ampicillin and ceftizoxime. Blood, urine and cerebrospinal fluid cultures, leukocyte count and C-reactive protein level were measured in all neonates. A total of 135 neonates were evaluated, 65 in amikacin group and 70 in ceftizoxime group. 60 neonates (85.7%) in ceftizoxime group and 54 neonates (83.1%) in amikacin group responded to the treatment (P= 0.673 and χ² = 0.178). Only 24 (18%) blood samples had a report of positive blood culture. The most frequent pathogen was coagulase negative staphylococcus with the frequency of 58.32% of all positive blood samples. Ceftizoxime in combination with ampicillin is an appropriate antimicrobial regimen for surrogating the combination of ampicillin and amikacin to prevent bacterial resistance against them. [ABSTRACT FROM AUTHOR]