Long-distance migratory flights are predicted to be associated with higher mortality rates when individuals encounter adverse weather conditions. However, directly connecting environmental conditions experienced in-flight with the survival of migrants has proven difficult. We studied how the in-flight mortality of 53 satellite-tagged Black-tailed Godwits (Limosa limosa limosa) during 132 crossings of the Sahara Desert, a major geographical barrier along their migration route between The Netherlands and sub-Saharan Africa, is correlated with the experienced wind conditions and departure date during both southward and northward migration. We show that godwits experienced higher wind assistance during southward crossings, which seems to reflect local prevailing trade winds. Critically, we found that fatal northward crossings (15 deaths during 61 crossings) were associated with adverse wind conditions. Wind conditions during migration can thus directly influence vital rates. Changing wind conditions associated with global change may thus profoundly influence the costs of long-distance migration in the future.