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Frequency domain analyses of changes in electromyographic (EMG) signals over time are frequently used to assess muscle fatigue. Fourier based approaches are typically used in these analyses, yet Fourier analysis assumes signal stationarity, which is unlikely during dynamic contractions. Wavelet based methods of signal analysis do not assume stationarity and may be more appropriate for joint time-frequency domain analysis. The purpose of this study was to compare Short-Time Fourier Transform (STFT) and Continuous Wavelet Transform (CWT) in assessing muscle fatigue in isometric and dynamic exercise. The results of this study indicate that CWT and STFT analyses give similar fatigue estimates (slope of median frequency) in isometric and dynamic exercise (P<;;003E;0.05). However, the results of the variance was lower for both types of exercise in CWT compared to STFT (P<;;0.05) indicating more variability in the EMG signal analysis using STFT. Thus, the stationarity assumption may not be the sole factor responsible for affecting the Fourier based estimates.