To evaluate the utility of endotracheal aspirate microscopy, culture and endotracheal tube tip culture for early diagnosis of ventilator-associated pneumonia in neonates. Inborn ventilated neonates were followed-up for ventilator-associated pneumonia using Center for Disease Control and Prevention (CDC) criteria. Endotracheal aspirate microscopy, culture and endotracheal tube tip cultures were performed. Ventilator-associated pneumonia occurred in 28/68 (41%) neonates as per CDC criteria. Endotracheal aspirate microscopy (≥5 polymorphonuclear cells per high power field) and endotracheal aspirate culture had 78.6% and 75% sensitivity, 87.5% and 90% specificity, positive predictive value of 81.5% and 84%, and negative predictive value of 85.4% and 83.72%, respectively. Mean (SD) time of result of microscopy and endotracheal aspirate culture was 55.7 (4.3) h and 108.3 (19.7) h, respectively in comparison to diagnosis made at 143.5 (23.3) h, as per CDC criteria. Endotracheal aspirate microscopic examination and culture can be supportive in objective diagnosis of ventilator-associated pneumonia with an added advantage of earlier prediction.