The aim of endotracheal aspiration is to eliminate secretions in patients with an artificial airway. All children with mechanical ventilation must undergo this procedure periodically. The frequency of aspiration depends on the type and quantity of the respiratory secretions and on the patient's clinical status. Aspiration should be performed by two people to maintain a greater degree of asepsis and to optimize stability of the airway and ventilation. Closed aspiration systems are available that allow aspiration without the need to disconnect the patient through a single probe that is constantly protected by a plastic sleeve and isolated from external environment. The most important risks of endotracheal aspiration are hypoxemia, mucosal injury, bronchospasm, arrhythmias, perforation of the airway with development of pneumothorax, accidental extubation, and infections. Bronchial brushing with a protected catheter and brochoalveolar lavage are used to analyze pulmonary infections. These techniques can be performed blind or through fibrobronchoscopy. They can also be used for the diagnosis of noninfectious pulmonary diseases such as alveolar proteinosis, alveolar hemorrhage or histiocytosis. Their adverse effects are similar to those of endotracheal aspiration.