Pulse oximeters require artifact-free clean photoplethysmograph (PPG) signals obtained at red and infrared (IR) wavelengths for the estimation of the level of oxygen saturation (SpO2) in the arterial blood of a patient. Movement of a patient corrupts a PPG signal with motion artifacts and introduces large errors in the computation of SpO2. A novel method for removing motion artifacts from corrupted PPG signals by applying Fourier series analysis on a cycle-by-cycle basis is presented in this paper. Aside from artifact reduction, the proposed method also provides data compression. Experimental results indicate that the proposed method is insensitive to heart rate variation, introduces negligible error in the processed PPG signals due to the additional processing, preserves all the morphological features of the PPG, provides 35 dB reduction in motion artifacts, and achieves a data compression factor of 12. © 2008 IEEE.