Guise’s forces occupied Paris and took control of the royal family while the Huguenots rose in the provinces, and their two commanders—Louis I de Bourbon, prince de Condé, and Admiral Gaspard II de Coligny—established headquarters at Orléans. The deaths of the opposing leaders—the Protestant Anthony of Bourbon, king consort of Navarra, and the Catholic marshal Jacques d’Albon, seigneur de Saint-André—and the capture of Condé caused both sides to seek peace. After the Battle of Dreux (December 1562) the war drew to a close, despite the assassination of the duc de Guise by a Protestant fanatic. A compromise was reached at the Peace of Amboise in March 1563: liberty of conscience was granted to the Huguenots, but the celebration of religious services was confined to the households of the nobility and to a limited number of towns.

The second war was precipitated by Huguenot fears of an international Catholic plot. Condé and Coligny were persuaded to attempt a coup to capture Catherine and Charles IX at Meaux in September 1567 and to seek military aid from the Protestant Palatinate. In the following brief war, the Catholic constable Anne, duc de Montmorency, was killed at the Battle of Saint-Denis (November 1567). The Peace of Longjumeau (March 1568) signaled another effort at compromise. This peace, however, proved little more than a truce; a third war soon broke out in September 1568. In an attempt to restore their authority, Catherine and King Charles dismissed L’Hospital in September and restored the Guise faction to favour. The edicts of pacification were rescinded; Calvinist preachers faced expulsion from France, and plans were made to seize Condé and Coligny. The former was killed at the Battle of Jarnac (1569), and the Huguenots were again defeated in that year at Moncontour. But the Catholic side failed to consolidate its successes, and yet another compromise was arranged at the Peace of Saint-Germain in August 1570.

Coligny subsequently regained the king’s favour but not the queen mother’s, and he remained an object of hatred with the Guises. In 1572 he was murdered. At the same time, some 3,000 Huguenots who gathered in Paris to celebrate the marriage of Margaret of Valois (later Margaret of France) to Condé’s nephew, Henry IV of Navarra, were massacred on the eve of the feast day of St. Bartholomew, and several thousand more perished in massacres in provincial cities. This notorious episode was the signal for the fifth civil war, which ended in 1576 with the Peace of Monsieur, allowing the Huguenots freedom of worship outside Paris. Opposition to these concessions inspired the creation of the Holy League, or Catholic League. Local Catholic unions or leagues had begun to appear in the 1560s, headed by nobles and prelates. In 1576, after the Peace of Monsieur with its concessions to the Huguenots, these local leagues were fused into a national organization. The league was headed by the Guise family and looked to Philip II of Spain for material aid. It sought, like the Protestants, to attract mass support; its clandestine organization was built around the house of Guise rather than the monarchy, from which it was increasingly alienated. In 1577 King Henry III (reigned 1574–89) tried to nullify the league’s influence, first by putting himself at its head and then by dissolving it altogether. This maneuver met with some success.

Renewed fighting broke out in 1577 between Catholic and Protestant noblemen, who defied Henry III in his attempt to assert royal authority. The Huguenots were defeated and forced by the Peace of Bergerac (1577) to accept further limitations upon their freedom. An uneasy peace followed until 1584, when, upon the death of François, duc d’Anjou, the Huguenot leader Henry of Navarra became the heir to the throne. This new situation produced the War of the Three Henrys (1585–89), during which the Guise faction—led by Henri I de Lorraine, 3^e duc de Guise—sought to have Navarra excluded from the succession. The threat of a Protestant king led to the revival of the Catholic League, which now took on a more radical form. This movement was centred in Paris among middle-class professional men and members of the clergy and soon spread among the Parisian artisans, guilds, and public officials. Henry III, who was considered far too tolerant toward the Huguenots, was an object of attack. In town after town, royalist officials were replaced by members of the league. In Paris the mob was systematically aroused; in 1588, on the famous Day of the Barricades (May 12), Henry III was driven from his own capital. In a welter of intrigue and murder, first the duc de Guise (December 1588) and his brother Louis II de Lorraine, 2^e cardinal de Guise (December 1588), and then Henry III himself (August 1589) were assassinated, allowing the Protestant Henry of Navarra (Henry IV) to ascend to the throne. After the murder of the Guises, the league came out in open revolt against the crown. Towns renounced their royal allegiances and set up revolutionary governments. In Paris, however, where the league was most highly organized, a central committee called the Sixteen set up a Committee of Public Safety and conducted a reign of terror in a manner similar to the much more famous one that occurred during the revolution 200 years later. Paradoxically, this genuinely populist and revolutionary element in the Holy League paved the way for the triumph of Henry IV (1589–1610), the first king of France from the house of Bourbon (a branch of the house of Capet). The aristocratic members of the league took fright at the direction in which the extreme elements in the movement were proceeding. Their fears reached a climax in 1591, when the Sixteen arrested and executed three magistrates of the Parlement of Paris. The growing split in the ranks of the members of the league, combined with Henry’s well-timed conversion to Roman Catholicism, enabled Henry to seize the initiative and enter Paris, almost unopposed, in 1594. In its final stages, the war became a struggle against Spanish forces intervening on behalf of Isabella Clara Eugenia, the daughter of Philip II of Spain and Elizabeth of Valois, who also laid claim to the French throne. The Peace of Vervins (1598), by which Spain recognized Henry IV’s title as king, and the Edict of Nantes of the same year, which granted substantial religious toleration to the Huguenots, ended the Wars of Religion.