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During migration, birds can show different responses to wind in relation to distance to the goal, experience, ecological barriers and visibility of landmarks. We analysed the effect of wind (tailwinds and crosswinds) on daily movement rates (forward and perpendicular) of Eleonora’s falcons using ARGOS satellite telemetry, during their trans-continental autumn migration to Madagascar, in relation to the different crossed regions and individuals’ age class. Our results showed that the effect of wind on daily movement rates was not uniform, being stronger in the farthest region from the migration goal, the Sahara desert, with adults being more affected than juveniles in this region. In the Sahel, the results were more conflicting, perhaps because daily movements were more shaped by the distribution of food resources. In Equatorial Africa, daily movement rates were mainly affected by crosswinds. Still, it remains unclear which orientation mechanism allows Eleonora’s falcons to reach such a narrow wintering area compensating also for wind displacement.