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Magnetite particles in the beak, cryptochromes in the eye, cellular ion-channel alterations, and changes in the vestibular system have been proposed to explain magnetoreception, but the exact mechanisms remain debated. Here, we used physical, morphological, functional, and genomic assays to identify the presence of superparamagnetic macrophages in the liver. We found that after macrophage depletion, pigeons flying under overcast conditions lacked their usual orientation capabilities. Orientation was unimpaired in birds without macrophages when the sun was visible, suggesting that this was their primary cue. 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