Christian was the eldest son of future king, Frederick I of Denmark, and Anna of Brandenburg. He was born at Gottorf Castle in Schleswig which Frederick I had made as a primary residence. In 1514, when he was just ten years old, Christian's mother died. Four years later, his father remarried to Sophie of Pomerania (1498–1568). In 1523, Frederick I was elected King of Denmark in the place of his nephew, King Christian II of Denmark. The young Prince Christian's first public service after his father became king was gaining the submission of Copenhagen, which stood firm for the fugitive, King Christian II. As stadtholder of the Duchies of Holstein and Schleswig in 1526, and as viceroy of Norway in 1529, Christian III displayed considerable administrative ability.
Christian's earliest teacher, Wolfgang von Utenhof (ca. 1495-1542) and his Lutheran tutor, the military general Johann Rantzau (1492–1565), were both zealous reformers who had an influence on the young Prince. At their urging, while traveling in Germany in 1521, he made himself present at the Diet of Worms to hear Martin Luther speak. Luther's arguments intrigued him. The Prince made no secret of his Lutheran views. His outspokenness brought him into conflict, not only with the Roman Catholic dominated State Council (Rigsraad), but also with his cautious and temporizing father. At his own court at Schleswig, he did his best to introduce the Protestant Reformation, despite the opposition of the bishops. He made the Lutheran Church the State Church of Schleswig-Holstein, with the Church Ordinance of 1528.
After his father's death, in 1533, Christian was proclaimed king at an assembly in Rye, a town in eastern Jutland, in 1534. The Rigsraad, dominated by Roman Catholic bishops and nobles, refused to accept Duke Christian as king and turned to Count Christopher of Oldenburg in order to restore Christian II to the Danish throne. Christian II had supported both the Roman Catholics and Protestant Reformers at various times. In opposition to King Christian III, Count Christopher was proclaimed regent at the Ringsted Assembly (landsting), and at the Skåne Assembly (landsting) on St Liber's Hill (Sankt Libers hög) near Lund Cathedral. This resulted in a two-year civil war, known as the Count's Feud (Grevens Fejde) from 1534–36, between Protestant and Catholic forces.
Count Christopher had the support of most of Zealand, Scania, the Hanseatic League, and the small farmers of northern Jutland and Funen. Christian III found his support among the nobles of Jutland. In 1534, peasants under Skipper Clement (c. 1484–1536) began an uprising in northern Jutland, pillaging the holdings of Lutheran nobles. An army of nobles and their vassals assembled at Svendstrup and suffered a terrible defeat at the hands of the peasants. Realizing his hold on the throne was in imminent danger, Christian III negotiated a deal with the Hansa States which allowed him to send his trusted advisor Johan Rantzau north with an army of Protestant German mercenaries. Clement and his army fled north, taking refuge inside the walls of Aalborg. In December, Rantzau's forces breached the walls and stormed the city. In the following days 3,000 people were massacred and the city was plundered by the Protestant German mercenaries. Clement managed to escape the slaughter, but was apprehended a few days later. He was tried and beheaded in 1535.
With Jutland more or less secure, Christian next focused on gaining control of Scania. He appealed to the Protestant Swedish king Gustav Vasa for help in subduing the rebels. Gustav immediately obliged by sending two armies to ravage central Scania and Halland. The peasants suffered a bloody defeat at Loshult in Scania. The Swedes moved against Helsingborg Castle, which surrendered in January 1535 and was burned to the ground.