Their first male child was stillborn (1674), and numerous others died in infancy or early childhood. Following James's accession to the throne in 1685, the question of whether Mary would ever bear a son became more significant, because such a child would be brought up in the Roman Catholic faith and would be heir to the throne.
In 1688, Mary finally gave birth to a living son, James. The event caused much speculation. It was suggested that the child had been born dead and a changeling smuggled into the room in a warming pan in order to conceal the death, or that the Queen had never actually been with child. Broadsheets depicting the queen stuffing pillows into her gown or cuckolding her husband with her confessor were common. For political reasons, a royal birth was a very public event, and many people would have had to be privy to this unlikely conspiracy. Nevertheless the rumours were disquieting enough that James called two extraordinary sessions of his Privy Council to hear testimony proving that the young Prince of Wales was his son by the Queen, though James's daughters disputed the child's legitimacy.
In exile, as guests and dependents of Louis XIV at the Chateau of Saint-Germain-en-Laye, Mary gave birth to one more child, Princess Louisa Maria, who died of smallpox at the age of nineteen.
Queen Mary died in Château de Saint-Germain-en-Laye near Paris of breast cancer. Her tomb, in the abbey of Chaillot, was destroyed during the French Revolution.
Mary's full style during James's reign was: "Her Majesty Mary, by the Grace of God, Queen of England, Scotland, France and Ireland"
| Name | Birth | Death | Notes |
|---|---|---|---|
| Catherine Laura | 10 January 1675 | 3 October 1676 | died of convulsions. |
| Isabel | 28 August 1676 | 2 March 1681 | |
| Charles, Duke of Cambridge | 7 November 1677 | 12 December 1677 | died of smallpox |
| Elizabeth | 1678 | c. 1678 | |
| Charlotte Maria | 16 August 1682 | 16 October 1682 | died of convulsions |
| James, Prince of Wales Old Pretender | 10 June 1688 | 1 January 1766 | married 1719, Maria Klementyna Sobieska; had issue |
| Louise | 28 June 1692 | 20 April 1712 |