In this work, the authors aimed to detect the clonal relatedness of the isolated imipenem-susceptible and non-susceptible Acenitobacter baumanii. This study was conducted from September 2008 through August 2009 in Aboelreech-Elmounira paediatric-Cairo University-teaching hospital in Egypt. All the isolated acenitobacter species were identified by standard laboratory procedures. The clonal relationship of the A. baumanii (the most common detected clinical type) was studied by biotyping and AST and then confirmed using rep-PCR with primers aimed at repetitive extragenic palindromic sequences and enterobacterial repetitive intergenic consensus sequences. A total of 100 A. baumanii isolates out of 104 acenitobacter species were recovered from different clinical samples. Sixty two percent of the isolates were resistant to imipenem. The resulting rep-PCR patterns of the A. baumanii strains revealed 8 clones, 3 clones found in the imipenem resistant group, and 5 clones in imipenem sensitive group with statistically significant clonal distribution in both groups (P-value 0.00). Clonality was proved in imipenem resistant group with an alarming predominance of clone 1 representing 80.6% of IMP-R isolates. In accordance the prevalence of resistant acenitobacter strains seems to be correlated with inappropriate antibiotic use. These results call for strict compliance of coordinated strategy of infection control measures and judicious use of antimicrobials which is likely to effectively deal with this serious public health issue.