Abstract: A method and system for managing mechanical ventilation of patients with respiratory disorders is described. The main objective of the system is to generate executable instructions for patient care which take into account a large number of parameters of patient condition and ventilation. Data regarding the state of the patient are stored in a database. Patient data are processed according to a set of protocols which contain rules for patient care decisions arranged in a logical sequence to generate detailed, executable instructions for patient care. Instructions are updated when new data are entered into the database. The data can be acquired in an automated fashion, or the clinician can be instructed to collect and enter new data into the clinical database. Likewise, patient care instructions can be carried out automatically or manually, but it is preferred that instructions are carried out manually as a safety check.