A stone detection system of a harvester that automatically changes its sensitivity to signals from a stone sensor in response to the type of harvesting equipment connected to the harvester is provided. The stone detection system generally includes a stone sensor, a header sensor and a microprocessor. The stone sensor is configured to generate a signal indicative of the presence of a stone in the crop harvesting system. The header sensor is disposed on the crop harvesting system to sense the header type and to generate a signal indicating the header type. The microprocessor is coupled to the stone sensor and the header sensor to process the stone sensor signal based at least in part upon the header sensor signal.