At Gatwick, BA's contingency plans, which include using pilots as cabin crew and leasing ready-crewed aircraft, meant four out of five flights before 1600 GMT went ahead.
For Glasgow the figure was 9 cancellations out of 37 flights, while at Manchester there were 14 cancellations out of 38 in total on BA's online schedule.
Speaking to striking cabin crew at a rally near Heathrow, Unite's joint leader Tony Woodley said the dispute was costing the airline "an arm and a leg".
He said a fresh offer recently put forward by British Airways had been rejected as "not good enough" for cabin crew. But he said the union was still willing to negotiate and urged BA to "come back" to the negotiating table.
Mr Woodley confirmed that he had been talking to Gordon Brown about the strike and was grateful for his attempts to encourage the two sides to reach a negotiated settlement.
According to his spokesperson, the Prime Minister was keeping "very closely in touch" with the situation and was very conscious of the impact the dispute was having on passengers.
AT THE SCENE
By Louisa Baldini, BBC News, near Heathrow
Red and white Unite banners and flags are peppered across the car park of a little football club on the outskirts of Heathrow, where strikers have been gathering for three days.
"Willie liar, pants on fire" they chant, referring to the airline's chief executive Mr Walsh. The crowd of between two and three hundred have been more vocal today than over the weekend, boosted by a visit and rousing talk from one of their union's leaders, Tony Woodley. "After three days of being here, we needed that boost", one of the strikers tells me. "There is a real feeling of solidarity."
As for the possibility of a settlement, most strikers I speak to believe the only hope is if negotiations by-pass Willie Walsh. Otherwise they are resigned to returning to the picket lines on Saturday. "We'd rather not, we'd rather be at work, but if we have to, we will."
The next round of industrial action will begin on 27 March, bringing with it more disruption if a resolution cannot be reached before then.
In the meantime, BA said the current three-day stoppage would continue to affect its operations this week after cabin crew return to work.
"We are sorry for any cancellations, as we get our aircraft, pilots and cabin crew back into the correct positions around the world," the airline said in a statement.
"We are contacting customers and offering them a full refund, a rebook or a re-route so that they can get to their destinations."
But it said the "vast majority" of passengers would be unaffected.
"The knock-on impact at Heathrow is far less than anticipated due to the numbers of cabin crew who came to work as normal over the past weekend."
The Unite union argues that the actual number who turned up for work is much lower than BA claims.
Cuts and losses
The strike action is the latest episode in a long-running dispute over changes to pay and conditions by BA that Unite claims are being unfairly imposed on its members.
Workers are particularly angry that last November BA reduced the number of crew on long-haul flights and is introducing a two-year pay freeze from 2010.
The airline also proposed new contracts with lower pay for fresh recruits.
BA suffered a loss before tax of £342m for the nine months to the end of December 2009 and says it needs to cut costs in order to survive.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.