Methods and systems for performing capture threshold tests are described. During an initialization procedure a capture detection interval and capture detection threshold are determined based on peak values of cardiac signals sensed following the supracapture threshold initialization pulses. Following initialization, a plurality of pacing pulses to the atrium are delivered and the peak values of the cardiac signals sensed following each of the plurality of pacing pulses are determined. The peak values are compared to the pacing artifact threshold and the capture detection threshold. A timing of each of the peak values is compared to the capture detection interval. For each pacing pulse, discrimination between a captured response, a noncaptured response, and a fusion response is based on the peak value and timing comparisons.