Lufthansa estimates it will have to cancel at least 500 flights across Europe on the Cityline and Eurowings airlines, according to a spokesperson in Frankfurt on Wednesday.
Pilots' union Cockpit called the warning strikes for some 1,000 pilots on Tuesday in an ongoing wage dispute after salary talks broke down with management.
Cockpit said all of Germany's major airports served by Eurowings and Cityline were affected, including Frankfurt, Munich, Düsseldorf and Berlin's Tegel airport.
The walk-outs began at midday Tuesday and were to continue until Wednesday at midnight.
Lufthansa has said it is attempting to book passengers on Deutsche Bahn trains instead. Passengers can exchange their plane tickets for train tickets if they like, the airline said.
The strikes are planned to continue until midnight Wednesday.
Lufthansa has offered Cockpit pilots a salary increase of 5.5 to 6.5 percent in the coming 18 to 24 months, but the organization has said the offer is too low.