Twenty-eight days after Alexander II's election an assembly of German and Lombard bishops and notables opposed to the reform movement was brought together at Basel by the Empress Agnes as regent for her son, Emperor Henry IV (1056–1105), and was presided over by the Imperial Chancellor Wilbert. They elected on 28 October 1061, the bishop of Parma, Cadalus, who assumed the name of Honorius II.

With the support of the Empress and the nobles, in the spring of 1062 Honorius II, with his troops, marched towards Rome to claim the papal seat by force. Bishop Benzo of Alba helped his cause as imperial envoy to Rome, and Cadalus advanced as far as Sutri. On 14 April a brief but bloody conflict took place at Rome, in which the forces of Alexander II lost and antipope Honorius II got possession of the precincts of St. Peter's.

Duke Godfrey of Lorraine arrived in May 1062, and induced both rivals to submit the matter to the King's decision. Honorius II withdrew to Parma and Alexander II returned to his see in Lucca, pending Godfrey's mediation with the German court and the advisers of the young German King, Henry IV.

In Germany, meanwhile, a revolution had taken place. Anno, the powerful Archbishop of Cologne, had seized the regency, and the Empress Agnes retired to the convent at Fructuaria in Piedmont. The chief authority in Germany passed to Anno, who was hostile to Honorius II.

Having declared himself against Cadalus, the new regent at the Council of Augsburg, (October 1062), secured the appointment of an envoy to be sent to Rome for the purpose of investigating charges of simony against Alexander II. The envoy, Burchard II, Bishop of Halberstadt (Anno's nephew) found no objection to Alexander II's election. Alexander II was recognized as the lawful pontiff, and his rival, Cadalus (Honorius II), excommunicated in 1063.

The antipope did not, however, abandon his claims. At a counter-synod held at Parma he defied the excommunication. He gathered an armed force and once more proceeded to Rome, where he established himself in the Castel Sant'Angelo.

The ensuing war between the rival Popes lasted for about a year. Honorius II eventually gave up, left Rome as a fugitive, and returned to Parma.

The Council of Mantua, on Pentecost, 31 May 1064, ended the schism by formally declaring Alexander II to be the legitimate successor of St. Peter. Honorius II, however, maintained his claim to the papal chair to the day of his death in 1072.