The increase was less than at some of the country's regional airports and follows a decision to transfer some domestic flights to Stansted.
The total rise in passenger numbers at Britain's airports last month was 11.5 million, a 4.5 per cent increase on September 1998.
Airport operator BAA said 115.7 million passengers have used its airports so far this year.
The largest single airport market increase was a 114.4 per cent rise in European scheduled traffic at Stansted. BAA said the Essex airport continued to outperform its other airports with passenger numbers rising 42.4 per cent to just over one million in September.
Edinburgh Airport saw passenger numbers jump 12 per cent to 487,000. Heathrow saw a small 0.6 per cent rise as the devastation caused by Hurricane Floyd affected flights to the US east coast.
Gatwick's increase was largely due to demand for flights to North America, the Channel Islands and long-haul destinations.
BAA chief executive Mike Hodgkinson said the rise in passenger numbers in September helped boost the total growth for the group's financial year so far by 5 per cent, reaffirming its predictions for annual growth of between 4.5 per cent and 5 per cent.
Scheduled flights to Europe were the most popular among passengers, rising 7.3 per cent to 3.9 million from 3.6 million in September last year. Ireland was also popular, rising 6.4 per cent, while flights to long-haul destinations jumped by 5.5 per cent.
Domestic traffic growth across BAA's London airports was flat following a 2.4 per cent drop at Heathrow after it and Gatwick transferred domestic flights to Stansted, where UK traffic grew by 17.3 per cent.
Converted for the new archive on 30 June 2000. Some images and formatting may have been lost in the conversion.
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