A method for fast median filtering in an implantable medical device is disclosed that provides rapid filtering using computational mechanisms with following elements. A new sample value is received into a buffer. An oldest sample value location is identified in a MIN-heap and a MAX-heap. A new sample value location is identified in either the MIN-heap or the MAX-heap by comparing the new sample value to a median value. The new sample value is placed into the oldest sample value location, if the MIN-heap or MAX-heap identified for the new sample value location is the same as the MIN-heap or MAX-heap identified for the oldest sample value location. A MIN-heap top or MAX-heap top is moved from the heap not containing the oldest value into the location of the oldest sample and the new sample is placed into the location of the MIN-heap top or MAX-heap top moved from the heap not containing the oldest value, if the heap identified for the new sample is not the same as the heap identified for the oldest sample. The MAX-heap is rebalanced so the MAX-heap top contains the highest value in the MAX-heap and the MIN-heap is rebalanced so the MIN-heap top contains the lowest value in the MIN-heap. The median value is calculated by averaging the MIN-heap top plus the MAX-heap top. The method for fast median filtering in an implantable medical device can also be expressed as a computer software product that includes a medium readable by a processor.