Background and aims: Today there is a controversy concerning the frequency to apply the ET suctioning, such as its impact on the duration of the respiratory support, the length of stay in the PICU, the incidence of infections associated to the health care and the accidental extubations. Objective: To compare whether there exist differences between morbidity, days of mechanical ventilation, length of stay in the PICU, incidence of Ventilator-Associated Pneumonia, and mortality, when two endotracheal suctioning protocols are performed. Design: Randomized controlled trial. Setting: University Hospital Pablo Tobón Uribe, Medellin-Colombia Patients: Ninety-two children with over a month old with mechanical ventilation in PICU. Interventions: As-needed endotracheal suctioning protocol and a routine suctioning protocol. Measurements: Composite primary end point was the presence of hypoxemia, arrhythmias, accidental extubation and heart arrest. The Relative Risk for the main outcome was obtained by a logistic function trough generalized estimating equations (GEE). Results: Characteristics of patients were similar between groups. Forty-five children underwent an as-needed endotracheal suctioning protocol and forty five underwent a routine endotracheal suctioning protocol. Primary main outcome was present in 22 (47%) and 25 (55%) children from intervention and control group respectively (RR=0.84; CI95% 0.56–1.25), as well in 35 (5.8%) from 606 endotracheal suctioning performed to intervention group and 48(7.4%) from 649 performed to control group (OR=1.30; CI95% 0.7–2.1). Conclusions: This study suggests that there is no difference in side effects between an as-needed and a routine endotracheal suctioning protocol.