He was born at Hohenems, the second son of the noble Wolf Dietrich von Ems (1507-1538).
A courtier of Charles V, Holy Roman Emperor and Chiara Medici, sister of Giovanni Angelo Medici (Pope Pius IV), Markus Sitticus was the brother of Jakob Hannibal von Hohenems, a general of Charles V and of Philip II of Spain; he was a cousin of Charles and Federico Borromeo and uncle of both Wolf Dietrich von Raitenau and Markus Sitticus IV von Hohenems, who were Prince-Bishop of Salzburg in 1587-1612 and 1612-1619, respectively.
From 1550 Markus Sittich von Hohenems was a member of the company headed by his uncle Gian Giacomo Medici, marchese di Melegnano, one of the last of the Renaissance condottieri. In 1552 he participated in Charles V's efforts to win Metz back from France, and in 1554/55 he was present at the siege of Siena and repulsed a Turkish attack on the Tuscan port of Piombino.
His uncle Giovanni Angelo Medici was raised to the papacy at the end of 1559 and, having assumed the tiara 6 January 1560 as Pius IV, proved generous in dispensing benefices to his Italian and German nephews: Marco Sittico was made bishop of Cassano, 29 May 1560. With other members of the German branch of the family relocated in Italy, he adopted the surname Altemps as an equivalent of Hohenems. In the Holy Roman Empire the Hohenems were raised to the rank of Reichsgrafen by Emperor Ferdinand I, 27 April 1560. Markus Sittikus was made a cardinal at the consistory of 26 February 1561.
With papal support he was named co-adjutor to the ailing Bishop of Constance, Christoph Metzler, whom he succeded in the see. Though he lacked theological training, he served as a papal legate to the Council of Trent, and served in diplomatic capacities Pius V, Gregory XIII and Sixtus V.
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