The monarch was at one of her palaces outside London in Windsor Castle for her big day, where she and husband Prince Philip took a round of the town in an open top royal vehicle, waving at cheering crowds of thousands of her subjects lined up on the streets.
She sliced into a three-tier birthday cake created by Bangladeshi-origin British chef Nadiya Hussein, winner of the 'Great British Bake Off' show, especially for the 90th celebrations as the crowds sang 'Happy Birthday'.
The Queen, dressed in a spring green outfit, remarked that it was a "lovely day" as she unveiled a plaque marking "The Queen's Walkway" at the foot of Castle Hill during a walkabout the town of Windsor.
The Walkway was designed by the UK's Outdoor Trust to symbolically recognise the moment that Elizabeth II became Britain's longest reigning monarch on September 9, 2015 after more than 63 years on the throne, linking 63 significant points in Windsor.
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Prime Minister David Cameron led the tributes by referring to the Queen as a "Rock of strength" while Prince Charles, the Queen's heir, recorded a special birthday message for his mother in which he reads an edited passage from William Shakespeare's Henry VIII for radio broadcast during the day.
In London, the King's Troop Royal Horse Artillery staged a 41-gun salute at midday in Hyde Park. The Honourable Artillery Company fired a 62-gun salute across the Thames from the Tower of London at an hour later.
After the Queen lights the first beacon in Windsor, more than 900 beacons across the UK and the Commonwealth will be lit up to mark her birthday.
Members of the UK's Army cadet force will take beacons to the top of the highest peaks of England, Scotland, Wales and Northern Ireland.
He said Britain was "uniquely blessed" to have her and praised the Queen's "unshakeable sense of duty".
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Royal Mail yesterday issued a set of 10 special stamps to mark the occasion, featuring four generations of UK monarchy with the Queen, Prince Charles, Prince William and Prince George.
The group family photograph taken last year appears as a stamp sheet, with perforations positioned to create a first class stamp for each of the four royals.
The Queen's official birthday celebrations for the nation are scheduled for the second weekend of June, which will include a grand charity street party near Buckingham Palace.
The queen was born Princess Elizabeth on April 21, 1926 and became queen on the death of her father, King George VI, in 1952. A majority of Britons have lived under no other monarch.