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| Manuel I |
| Children include |
| Miguel da Paz, Prince of Portugal and of Asturias |
| João, Prince of Portugal (future John III) |
| Isabella, Holy Roman Empress |
| Infanta Beatriz, Duchess of Savoy |
| Infante Luís, Duke of Beja |
| Infante Fernando, Duke of Guarda and Trancoso |
| Cardinal-Infante Afonso |
| Henry I |
| Infante Duarte, Duke of Guimarães |
| Infanta Maria, Lady of Viseu |
| Grandchildren include |
| Philip II of Spain and I of Portugal) |
| Anthony I (illegitimate) |
| Infanta Maria of Guimarães, Duchess of Parma and Piacenza |
| Infanta Catarina of Guimarães, Duchess of Braganza |
| Great-Grandchildren include |
| Teodósio II, Duke of Braganza |
| Ranuccio I Farnese of Parma |
| Great-Great-Grandchildren include |
| John II, Duke of Braganza (future John IV) |
| John III |
| Children include |
| Maria Manuela, Princess of Portugal and of Asturias |
| João Manuel, Prince of Portugal |
| Grandchildren include |
| Sebastião, Prince of Portugal (future Sebastian I) |
| Carlos, Prince of Asturias |
| Sebastian |
| Henry |
| Anthony (disputed king) |
