At CHES 2006, a DPA countermeasure based on the Fourier Transform was published. This generic countermeasure aims at protecting from DPA any S-box calculation used in symmetric cryptosystems implementations. In this paper, we show that this countermeasure has a flaw and that it can be broken by first order DPA. Moreover, we have successfully put into practice our attack on two different S-box implementations. Finally, we propose an improvement of the original countermeasure and we prove its security against first order DPA.