The three men were charged with conspiring between November 1, 2004 and June 29, 2005 to cause explosions on London's transport network "and/or tourist attractions in London of a nature likely to endanger life or cause serious injury".
The three men were due for an initial court appearance Saturday.
Peter Clarke, a senior officer within the London Metropolitan Police's anti-terrorism branch, said he expected that further arrests would be made as the investigation continued.
"The detail of the evidence must wait, but it is probably fair to describe it as a complicated jigsaw with thousands of pieces," Clarke said.
"We now have enough of the pieces in the right place for us to see the picture, but it is far from complete. Because of that, the search is not over."