Hergenröther was one of the eight who sent in a written protest against the opening discourse of Döllinger on the past and present of Catholic theology. Among the other signers were Heinrich Moufang von Schäzler, Paul Leopold Haffner, Franz Hettinger, and Matthias Joseph Scheeben. Hergenröther was soon called on to answer the pamphlet of Dr. Friedrich Bernhard Ferdinand Michelis, Kirche oder Partei? Ein offenes u. freies Wort an den deutschen Episkopat (Church or Faction? A Frank Address to the German Episcopate), in which this writer attacked violently the "Mainz" and the "Roman" theologians. Hergenröther's answer appeared in the "Chilianeum" (1865) under the title of Kirche u. nicht Partei. Eine Antwort auf die jüngste Broschüre des Herrn Dr. Fr. Michelis (Church and not Faction: an Answer to the latest Brochure of Dr. Michelis). In the same review (1863) Hergenröther had written a critical account of the latest efforts of Western Catholics for ecclesiastical reunion with the Oriental Churches. The opening of the Vatican Council (1870) brought to a head the domestic conflict in Germany. Hergenröther was the foremost defender of the council and its decrees; as early as 1868 he had been appointed, with Hettinger, consultor for the preparation of the council's work and had taken up his residence at Rome. His knowledge of ecclesiastical history, canon law, and Catholic dogma made him a valuable co-labourer in the many careful and detailed preliminary meetings of the council commission. In the meantime he prepared, with Hettinger, and published in the "Chilianeum" (1869) a memorial of the theological faculty of Würzburg in reply to five questions, submitted by the Bavarian Government, concerning the approaching council. He also published (Der Katholik, 1871) another outlined memorial concerning the Vatican Council, in reply to eleven questions submitted by the Bavarian Minister of Worship to the theological and law faculties of Würzburg. This memorial, though projected, was never formally called for by the Government. The opposition to the Vatican Council reached its acme in the work Der Papst und das Concil, by "Janus" (Döllinger). In the same year (1869) Hergenröther prepared his "Anti-Janus", an historico-theological critique (Freiburg, 1870). He also published a number of small brochures in favour of the council and against Döllinger, e. g. "Die Irrthümer logischer Censor" (Freiburg, 1870), and a critique of Dr. Döllinger's declaration of 28 March 1871 (Freiburg, 1871). His pen was also active in the "Historisch-politische Blätter", where he published