Lufthansa has cancelled 3800 flights during the strike, which runs until the end of Friday, and says the stoppage will cost it tens of millions of euros.The pilots' walkout is the third strike to hit Frankfurt Airport in six weeks after action by security staff and public sector workers.
With many flights cancelled in advance, Lufthansa passengers mostly stayed away.
Check-in desks at Frankfurt, the airline's home base, were being used as rebooking desks instead. But queues were short and many had already rebooked online.
Those passengers at the airport seemed satisfied with the service being offered. Lufthansa says it is able to run around 500 flights over the three days, just more than 10% of its normal service.
Markus Wahl, of the pilots' union, said: "This is a massive attack on our rights."