A short service was held with around 100 MPs and peers, and parliamentary and Downing Street staff taking part.
The union jack-draped coffin had arrived earlier in an escorted hearse.
Meanwhile, MPs have voted to cancel Prime Minister’s Questions on Wednesday, after some MPs had tried to force it to go ahead.
Margaret Thatcher, who died at the age of 87 on April 8, has been accorded a ceremonial funeral with military honors, one step down from a state funeral.
Baroness Thatcher’s body will now rest overnight in the Palace of Westminster’s Chapel of St Mary Undercroft, where a service was led by the Dean of Westminster for members of the family, senior figures from both Houses of Parliament, and staff from Parliament and Downing Street.
Senior figures attending included Commons Speaker John Bercow, Leader of the House Andrew Lansley, Chief Whip Sir George Young and Work and Pensions Secretary Iain Duncan Smith.
Senior Liberal Democrat Baroness Williams said the service had been “very impressive” and “not at all political” but “more about the Thatcher family”.
Conservative MP Sir Gerald Howarth added that it had been “dignified”.
The chapel will be open for several hours in order that members of both Houses and parliamentary staff may pay their respects.
The House of Commons Speaker’s chaplain will then keep vigil through the night.
A debate in the Scottish Parliament on Margaret Thatcher’s legacy is to be postponed until after the funeral.
Green Party and independent members had wanted to hold the discussion shortly after the service, but the main parties at Holyrood have agreed that it should be moved to Thursday.
On Wednesday morning, Margaret Thatcher’s coffin will initially travel by hearse from the Palace of Westminster to the Church of St Clement Danes – the Central Church of the RAF – on the Strand.
The coffin will then be transferred to a gun carriage and taken in procession to St Paul’s.
Queen Elizabeth II and the Duke of Edinburgh are among more than 2,000 people expected to attend the service.
Former US Vice-President Dick Cheney and ex-Secretary of State Henry Kissinger will also be among the guests, while 4,000 police will be on duty.
Barack Obama’s official presidential delegation will be led by George Shultz and James Baker, who both served as secretaries of state during the Thatcher era.
Argentina’s ambassador to London, Alicia Castro, has declined an invitation to attend.
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