We investigated the risk associated with crossing the Sahara Desert for migrating birds by evaluating more than 90 journeys across this desert by four species of raptors (osprey Pandion haliaetus, honey buzzard Pernis apivorus, marsh harrier Circus aeruginosus and Eurasian hobby Falco subbuteo) recorded by satellite telemetry. Forty per cent of the crossings included events of aberrant behaviours, such as abrupt course changes, slow travel speeds, interruptions, aborted crossings followed by retreats from the desert and failed crossings due to death, indicating difficulties for the migrants. The mortality during the Sahara crossing was 31 per cent per crossing attempt for juveniles (first autumn migration), compared with only 2 per cent for adults (autumn and spring combined). Mortality associated with the Sahara passage made up a substantial fraction (up to about half for juveniles) of the total annual mortality, demonstrating that this passage has a profound influence on survival and fitness of migrants. Aberrant behaviours resulted in late arrival at the breeding grounds and an increased probability of breeding failure (carry-over effects). This study also demonstrates that satellite tracking can be a powerful method to reveal when and where birds are exposed to enhanced risk and mortality during their annual cycles.