The Duke of Edinburgh, Prince Philip, was missing by the Queen's side this time as he continues to recover from an abdominal surgery in hospital.
More than 1,000 soldiers and horses took part in the traditional display of pomp and pageantry which celebrates the British monarch's official birthday.
The Queen's actual birthday was on April 21, when she turned 87.
Prince Philip, 92, is expected to remain at the London Clinic on Harley Street for a further week, followed by a period of convalescence of about two months.
The Queen later visited Prince Philip at the private London clinic where he has been since an exploratory operation on his abdomen on June 7.
She arrived alone as she made the visit "quietly and privately", a Buckingham Palace spokesperson said.
This year is only the third time that Prince Philip has missed the event after not attending in 1962 and 1968 when he was away on royal tours.
Prince William's wife, Catherine, the Duchess of Cambridge, made her last public engagement before her baby is born in mid-July.
The military parade coincides with the announcement of the Queen's birthday honours list, which included British Indian sculptor Anish Kapoor in line for a knighthood this year.
The Queen was cheered by crowds as she travelled to Horse Guards Parade in a vintage carriage along The Mall, leaving Buckingham Palace in the morning.
The glass coach was built in 1881 as a town coach for the Lord Mayor of London and was purchased for King George V's coronation in 1911.
It has been used in many royal weddings, including the Queen's marriage to Prince Philip in 1947 when she was still Princess Elizabeth.
Thousands lined the streets of London to watch the Queen take the royal salute and more than 1,000 soldiers and horses took part in the traditional parade.
Prince William and his father, Prince Charles, also took part on horseback.
The "Colour" paraded this year was that of the 1st Battalion Welsh Guards, who recently returned from service in Afghanistan.
The royal event ended with a 41-gun salute, fired by the King's Troop Royal Horse Artillery in Green Park, near the palace, to mark the Queen's official birthday.
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