A capture detection algorithm detects and distinguishes atrial capture. Atrial chamber reset (ACR) and AV conduction (AVC) algorithms are implemented to measure an atrial pacing threshold The data that is used to choose between ACR and AVC methods is used to determine the progression of the patient's disease state. Some of the significant aspects of the invention include enablement of accurate threshold measurements, including calculation of stability criteria, precise interval measurements and the use of reference interval to determine capture and loss of capture.