A method and system for detecting T-wave alternans for use in an implanted medical device uses wave transformation of QT intervals to obtain a reliable measure of TWA. In one embodiment, an array provides alternating sign multiplication factors which are applied respectively to n consecutive QT values. Each successive QT value is high pass filtered and moved sequentially through a queue so that each cycle each of the n QT values is multiplied by one of the factors; the products are summed and made absolute to provide an alternans match value. The alternans match is compared with a noise threshold signal, and alternans is declared when the match exceeds the threshold by a predetermined amount. The array is programmable and can be varied, providing a high degree of flexibility to optimize the test for the patient.