Two of the men, aged 23 and 30, were arrested at Manchester airport as they were about to fly to Pakistan. A third, aged 26, was seized at a house in Leeds.
The suspects, all believed to be British born of Pakistani heritage, are understood to have been under surveillance for several months by the police and MI5. They were being investigated for either offering support, or having knowledge of the four British-born extremists who carried out the rucksack bombings on the London transport system in 2005 which killed 52 people.
The two men detained at the airport at 1pm, were seized because, it is thought the police suspected they may not return to Britain. The third man was arrested at 4pm. They were all arrested on suspicion of the commission, preparation, or instigation of acts of terrorism under the Terrorism Act 2000.
Searches were being coducted at five houses in the Beeston area of Leeds, which is where the ringleader of the suicide cell and his deputy lived. A flat and a separate business premises were also being searched in east London.
A counter-terrorism source said: "Our investigations have been ongoing since the attacks on 7 July. We have been seeking answers to the questions of whether anyone else knew about the plans to carry out the attacks, helped or encouraged them.
"These arrests and searches are looking for answers to those questions.
"We are not looking for any more bombers - that is not what this is about."
Scotland Yard said the arrests were part of a pre-planned operation and also involved the West Yorkshire counter terrorism unit.
The significance of yesterday's arrests was unclear but a second anti-terrorism source said the suspects were being investigated for "possible association with some of the bombers".
"We are not talking about bomb plots," said the source.
The arrested men were taken to Paddington Green high security police station in central London where they will be interviewed by the Met's counter-terrorism command.
The police and MI5 have continued to deploy huge resources in investigating the background of the four suicide bombers - Mohammad Sidique Khan, 30, Shahzad Tanweer, 22, Hasib Hussain, 18, and Germaine Lindsay, 19.
Khan, the lead figure in the gang, and his deputy, Tanweer, both came from the Beeston area of Leeds. Hussain lived in Holbeck on the outskirts of the city. Lindsay grew up in Beeston but moved to Aylesbury in Buckinghamshire.
All four men died in the attacks. Tanweer killed seven people when he set off his bomb on a Tube train between Liverpool Street and Aldgate stations on the eastbound Circle line
Khan murdered six when he detonated his bomb on board a westbound Circle line train at Edgware Road
Twenty six were killed by Lindsay on a packed Piccadilly line train as it travels between King's Cross and Russell Square.
An hour later, 13 people died on the number 30 bus in Tavistock Square when Hussain set off his device.
Lord Carlile QC, the independent reviewer of terrorism legislation, said: "Anybody who imagined that this had simply been treated as four lone wolves, or a pack of wolves on 7 July 2005 was very wrong." He said a "rigorous hunt" was going on for everyone connected with the attacks and nobody involved could "lie easy in their beds".
A Scotland Yard spokesman said: "Detectives have continued to pursue many lines of inquiry both here in the UK and overseas. This remains a painstaking investigation with a substantial amount of information being analysed and investigated.
"As we have said previously, we are determined to follow the evidence wherever it takes us to identify any other person who may have been involved, in any way, in the terrorist attacks.
"We need to know who else, apart from the bombers, knew what they were planning. Did anyone encourage them? Did anyone help them with money, or accommodation?"
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