Flight directions and routes of migrating birds are determined by the birds' compass orientation, but also by effects of wind, social influence, responses to topography and landmarks, and to navigation cues. We investigated the orientation and routes taken by arctic shorebirds during autumn migration in southern Sweden at three different sites situated within a distance of 200 km from each other, in relation to the birds' destinations. We used three different methods, visual telescope observations, tracking radar registration and ring recoveries. Mean track directions differed significantly between the different sites in a way that demonstrated fine-scaled orientation changes when the shorebirds passed the southern Baltic region. The gradual change cannot be explained by different wind conditions at the different sites or by distinct responses to specific topographical features, i.e. the birds were not following coastlines or prominent landmarks in any detailed way. Neither could it be reconciled with orientation according to any of the main compass mechanisms known to be used by migrating birds which indicates that the control of flight courses and paths may be more complex than expected. The shorebirds might travel within a slightly winding flight corridor in broad agreement with the large-scale topography to maximize general association with coastal habitats during migration. Juvenile birds had a significantly different orientation than adults, particularly when the juveniles travelled in flocks without any adults. Juvenile birds may learn the general flight paths and course changes in relation to the large-scale topography from older and experienced individuals in the flocks, but most of this learning process between generations probably does not take place until after the birds' first autumn migration.