A weather warning issued by the emergencies ministry in Moscow predicted storms and strong winds of more than 50 miles per hour that could topple trees and bring down power lines.
At around 10 pm (1900 GMT), 73 flights were delayed and eight cancelled at Domodedovo airport to the south of the city, according to Yandex search engine's timetable service.
A further 40 flights were delayed and eight cancelled at the northern Sheremetyevo airport while eight were delayed at Vnukovo airport to the west, Yandex said.
Aeroflot carrier, based at Sheremetyevo, on Twitter warned passengers that "currently at Sheremetyevo due to complex weather conditions, flights are being delayed on arrival and departure."
It said that the weather conditions meant that it was impossible to use any transport on the airfield at times, causing delays with baggage deliveries.
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