By altering its flight altitude, a bird can change the atmospheric conditions it experiences during migration. Although many factors may influence a bird's choice of altitude, wind is generally accepted as being the most influential. However, the influence of wind is not clearly understood, particularly outside the trade-wind zone, and other factors may play a role. We used operational weather radar to measure the flight altitudes of nocturnally migrating birds during spring and autumn in the Netherlands. We first assessed whether the nocturnal altitudinal distribution of proportional bird density could be explained by the vertical distribution of wind support using three different methods. We then used generalized additive models to assess which atmospheric variables, in addition to altitude, best explained variability in proportional bird density per altitudinal layer each night. Migrants generally remained at low altitudes, and flight altitude explained 52 and 73% of the observed variability in proportional bird density in spring and autumn, respectively. Overall, there were weak correlations between altitudinal distributions of wind support and proportional bird density. Improving tailwind support with height increased the probability of birds climbing to higher altitude, but when birds did fly higher than normal, they generally concentrated around the lowest altitude with acceptable wind conditions. The generalized additive model analysis also indicated an influence of temperature on flight altitudes, suggesting that birds avoided colder layers. These findings suggested that birds increased flight altitudes to seek out more supportive winds when wind conditions near the surface were prohibitive. Thus, birds did not select flight altitudes only to optimize wind support. Rather, they preferred to fly at low altitudes unless wind conditions there were unsupportive of migration. Overall, flight altitudes of birds in relation to environmental conditions appear to reflect a balance between different adaptive pressures.