Background: Ventilator-associated pneumonia (VAP) is a frequent issue in intensive care units (ICU), with a major impact on morbidity, mortality and cost of care. VAP diagnosis remains challenging: traditional culture-based microbiological techniques are still the gold-standard, but are too slow to enable clinicians to improve prognosis with timely antimicrobial therapy adjustment. Aim: to compare the performance of the real time quantitative molecular based method versus conventional culture in diagnosis of ventilator associated pneumonia caused by P. aeruginosa in pediatric patients. Methods: this study included forty paediatric patients aged from one month to 18 years attending Paediatric Intensive Care Unit (PICU) and developed VAP during mechanical ventilation, All patients were subjected to full history taking, full clinical examination, chest X-ray, semiquantitative culture of BAL and ETA  on different routine bacteriological media for isolation of the causative organisms and molecular quantification for detection and quantification of P. aeruginosa in BAL and ETA samples by real -time PCR. Results: The mean age in patients' group was 40.7±31.6 months with male predominance (60%). PCR ETA can diagnose Pseudomonas aeruginosa in VAP, with 88.9% sensitivity, 90.3% specificity, 72.7% PPV and 96.5% NPV. AUC (95%CI) = 0.896 (0.76-1.0) and ROC curve analysis showed that PCR BAL can diagnose  Pseudomonas aeruginosa in VAP, with 100% sensitivity, 96.7% specificity, 90.9% PPV and 100% NPV. AUC (95%CI) = 0.983(0.94-1.0). Conclusion: Molecular biology makes it possible to obtain in the future quick and reliable microbiological results in patients with VAP. qPCR can provide reliable quantitative microbiological data, highly specific and with a good sensitivity for common pathogens involved in VAP.