Retinal images are used for diagnostic purposes by ophthalmologists. However, despite controlled conditions in acquisition retinal images often suffer from non-uniform illumination which hinder their clinical use. In this work we propose the compensation of the illumination by modeling the intensity as a sum of non-stationary signals using bidimensional empirical mode decomposition (BEMD). We compare the estimation and compensation of the background illumination with a widely used technique based retinal image pixel classification. The proposed method has shown to provide a better estimation of the background illumination, particularly in complicated areas such as the optic disk (usually bright) and the periphery of fundus images (usually dim).