Modern frequency power converters generate a wide spectrum of harmonic components. Large converter systems can also generate noncharacteristic harmonics and interharmonics. Standard tools of harmonic analysis based on the Fourier transform assume that only harmonics are present and the periodicity intervals are fixed, while periodicity intervals in the presence of interharmonics are variable and very long. In the case of frequency converters the periods of the main component are unknown. The Prony method as applied for signal analysis in power frequency converter was tested in the paper. The method does not show the disadvantages of the traditional tools and allow exact estimation the frequencies of all or dominant components, even when the periodicity intervals are unknown. To investigate the appropriateness of the method several experiments were performed. For comparison, similar experiments were repeated using the FFT. The comparison proved the superiority of the Prony method.