A system for estimating upper airway resistance or lung compliance, comprising: a pressure generating system; a patient circuit operatively coupled to the pressure generating system; and a controller operatively coupled to the pressure generating system, the controller being adapted to estimate the upper airway resistance or the lung compliance of a patient by: inducing a central apnea in the patient, wherein inducing the central apnea comprises causing the pressure generating system to provide a central apnea inducing stimulus to the patient and determining whether patient airflow has ceased; causing the pressure generating system to generate a known pressure stimulus comprising a flow of breathing gas having a known pressure level while the patient is experiencing the central apnea, wherein the known pressure stimulus is provided to the patient through the patient circuit; determining a patient flow-related parameter associated with the known pressure stimulus; and estimating the upper airway resistance or the lung compliance of the patient using the patient flow-related parameter; wherein causing the pressure generating system to generate a known pressure stimulus, determining the patient flow-related parameter and estimating the upper airway resistance or the lung compliance are performed only if it is determined that patient airflow has ceased a pressure generating system; a patient circuit operatively coupled to the pressure generating system; and a controller operatively coupled to the pressure generating system, the controller being adapted to estimate the upper airway resistance or the lung compliance of a patient by: inducing a central apnea in the patient, wherein inducing the central apnea comprises causing the pressure generating system to provide a central apnea inducing stimulus to the patient and determining whether patient airflow has ceased; causing the pressure generating system to generate a known pressure stimulus comprising a flow of breathing gas having a known pressure level while the patient is experiencing the central apnea, wherein the known pressure stimulus is provided to the patient through the patient circuit; determining a patient flow-related parameter associated with the known pressure stimulus; and estimating the upper airway resistance or the lung compliance of the patient using the patient flow-related parameter; wherein causing the pressure generating system to generate a known pressure stimulus, determining the patient flow-related parameter and estimating the upper airway resistance or the lung compliance are performed only if it is determined that patient airflow has ceased inducing a central apnea in the patient, wherein inducing the central apnea comprises causing the pressure generating system to provide a central apnea inducing stimulus to the patient and determining whether patient airflow has ceased; causing the pressure generating system to generate a known pressure stimulus comprising a flow of breathing gas having a known pressure level while the patient is experiencing the central apnea, wherein the known pressure stimulus is provided to the patient through the patient circuit; determining a patient flow-related parameter associated with the known pressure stimulus; and estimating the upper airway resistance or the lung compliance of the patient using the patient flow-related parameter; wherein causing the pressure generating system to generate a known pressure stimulus, determining the patient flow-related parameter and estimating the upper airway resistance or the lung compliance are performed only if it is determined that patient airflow has ceased