Pigeons were released at two sites of equal distance from the loft, one within a magnetic anomaly, the other in magnetically quiet terrain, and their tracks were recorded with the help of GPS receivers. A comparison of the beginning of the tracks revealed striking differences: within the anomaly, the initial phase lasted longer, and the distance flown was longer, with the pigeons' headings considerably farther from the home direction. During the following departure phase, the birds were well homeward oriented at the magnetically quiet site, whereas they continued to be disoriented within the anomaly. Comparing the tracks in the anomaly with the underlying magnetic contours shows considerable differences between individuals, without a common pattern emerging. The differences in magnetic intensity along the pigeons' path do not differ from a random distribution of intensity differences around the release site, indicating that the magnetic contours do not directly affect the pigeons' routes. Within the anomaly, pigeons take longer until their flights are oriented, but 5 km from the release point, the birds, still within the anomaly, are also significantly oriented in the home direction. These findings support the assumption that magnetically anomalous conditions initially interfere with the pigeons' navigational processes, with birds showing rather individual responses in their attempts to overcome these problems.Electronic supplementary materialThe online version of this article (doi:10.1007/s00114-011-0802-3) contains supplementary material, which is available to authorized users.