<p>Birds during migration depend on the situation aloft when flying and on the ground when refuelling. Side- and headwinds, precipitation and fog hamper flight, and hence the situation aloft has been incorporated in models of bird migration. However, there are hardly any studies about the effect of weather on fuel deposition rates during stopovers. Here, we investigated the effect of rain and wind speed on fuelling rates at a resting site in Switzerland in Garden Warbler <i>Sylvia borin</i>, Eurasian Blackcap <i>Sylvia atricapilla</i>, European Robin <i>Erithacus rubecula</i> and Pied Flycatcher <i>Ficedula hypoleuca</i> during autumn migration. Fuelling rates, estimated from plasma concentrations of triglycerides and uric acid, were lower during rain than without rain, increased after the end of rain, and decreased when wind speed increased. Comparison of the metabolite levels with data from earlier experiments suggested that birds just maintained or lost body mass during a rainy day (negative fuelling rates), and strong wind almost halved fuelling rates. Hence, when bad weather reduces food availability birds must choose between: (a) remain at stopover site and wait for better fuelling conditions while losing body mass, or (b) embark with reduced ground speed (in headwinds) and drift (with crosswinds) to a potentially better stopover site. The second option may explain the many observations of birds migrating under unfavourable weather conditions. If bad weather reduces food availability, the conditions on the ground and in-flight are linked and vary in parallel. However, if bad weather increases food availability, the link between conditions for stopover and in-flight is reversed. We conclude that a negative effect of bad weather on fuelling rates presents an additional challenge for migration which has been largely neglected.</p>