Many planes have been lost to thunderstorm encounters in which the plane broke apart in the turbulence. Not only can strong air motion break an airplane apart, but it can also cause a plane to lose altitude rapidly. This effect is referred to as a downdraft.

Flights are cancelled during thunderstorms not because the plane can't fly, but because of the severe risks associated with takeoff and landing. The most dangerous phenomenon is wind shear—a sudden change in wind speed or direction—and microbursts, which can slam an aircraft toward the ground with thousands of pounds of force. Lightning itself is rarely the cause of a cancellation, as modern planes act as "Faraday cages" that safely conduct the bolt around the exterior, but it can disable ground equipment and endanger the ramp crew who must stop refueling and baggage handling for safety. Furthermore, thunderstorms cause massive air traffic congestion; as planes divert to avoid storm cells, "holding patterns" fill up, and the FAA may implement a "Ground Stop" to prevent more planes from entering a dangerous area. If a storm is slow-moving and blocking the only available flight path, airlines will cancel the flight rather than risk running low on fuel while waiting for a window to open.