Rapid eye movements (REMs) are a prominent feature of REM sleep, and their distribution and time density over the night represent important physiological and clinical parameters. At the same time, REMs produce substantial distortions on the electroencephalographic (EEG) signals, which strongly affect the significance of normal REM sleep quantitative study. In this work a new procedure for a complete and automated analysis of REM sleep is proposed, which includes both a REMs detection algorithm and an ocular artifact removal system. The two steps, based respectively on Wavelet Transform and adaptive filtering, are fully integrated and their performance is evaluated using REM simulated signals. Thanks to the integration with the detection algorithm, the proposed artifact removal system shows an enhanced accuracy in the recovering of the true EEG signal, compared to a system based on the adaptive filtering only. Finally the artifact removal system is applied to physiological data and an estimation of the actual distortion induced by REMs on EEG signals is supplied.