Information about when and where animals die is important to understand population regulation. In migratory animals, mortality might occur not only during the stationary periods (e.g. breeding and wintering) but also during the migration seasons. However, the relative importance of population limiting factors during different periods of the year remains poorly understood, and previous studies mainly relied on indirect evidence. Here, we provide direct evidence about when and where migrants die by identifying cases of confirmed and probable deaths in three species of long-distance migratory raptors tracked by satellite telemetry. We show that mortality rate was about six times higher during migration seasons than during stationary periods. However, total mortality was surprisingly similar between periods, which can be explained by the fact that risky migration periods are shorter than safer stationary periods. Nevertheless, more than half of the annual mortality occurred during migration. We also found spatiotemporal patterns in mortality: spring mortality occurred mainly in Africa in association with the crossing of the Sahara desert, while most mortality during autumn took place in Europe. Our results strongly suggest that events during the migration seasons have an important impact on the population dynamics of long-distance migrants. We speculate that mortality during spring migration may account for short-term annual variation in survival and population sizes, while mortality during autumn migration may be more important for long-term population regulation (through density-dependent effects).