Neonatal septicemia remains one of the main causes of mortality and morbidity in neonates. Detection of neonatal sepsis quickly is critical as it is a life threatening condition. Molecular methods may offer advantages over conventional blood culture due to the rapidity and the small sample volume required for analysis. Molecular detection of bacterial sepsis was done by using specific primers (16 sRNA, rpoB and its). It was found that 16 sRNA genes were present in (20%) of samples and rpoB gene present in (18.8%). While its gene used for detection of fungi revealed a negative result in all samples.