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Conventional motion estimation does not take inter-frame brightness variations into consideration, which causes inefficient video coding for sequences involving brightness variations. H.264 provides a specific mode called weighted prediction targeting to improve the coding efficiency for this case. In this paper, we propose a Retinex based motion estimation scheme which effectively removes the inter-frame de-correlation factor resulting from brightness variations. We also propose to use some DCT techniques to generate the Retinex images for both current and reference images and apply conventional motion estimation and compensation procedures for coding. We applied the scheme to the H.264 testing the efficiency in the multiple reference frame motion compensation environment. Experimental results show that our proposed scheme outperforms the H.264 system with weighted prediction enabled. It allows the system to use a smaller number of reference frames for coding, e.g. 2, to achieve a similar (or slightly better) compression efficiency of the H.264 system using 5 reference frames.