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The theology of John Calvin has been influential on its influence on Calvinism and Protestant thought more generally. There has been disagreement among scholars regarding the degree to which later Calvinism corresponds to Calvin's own theology.

The Encyclopedia of Christianity suggests that

His theological importance is tied to the attempted systematization of Christian doctrine. In the doctrine of predestination; in his simple, eschatologically grounded distinction between an immanent and a transcendent eternal work of salvation, resting on Christology and the sacraments; and in his emphasis upon the work of the Holy Spirit in producing the obedience of faith in the regenerate (the tertius usus legis, or so-called third use of the law), he elaborated the orthodoxy that would have a lasting impact on Reformed theology.

Publications
Calvin developed his theology in his biblical commentaries as well as his sermons and treatises, but the most concise expression of his views is found in his magnum opus, the Institutes of the Christian Religion. He intended that the book be used as a summary of his views on Christian theology and that it be read in conjunction with his commentaries. The various editions of that work span nearly his entire career as a reformer, and the successive revisions of the book show that his theology changed very little from his youth to his death.

Scripture
Calvin expounded his view of Scripture in Book I of The Institutes of the Christian Religion. He viewed Scripture as necessary in that General revelation cannot in itself give us a saving knowledge of God, and authoritative in its being equivalent to an utterance of God given from heaven.

Calvin viewed Scripture as being both majestic and simple. According to Ford Lewis Battles, Calvin had discovered that "sublimity of style and sublimity of thought were not coterminous."

Atonement
R. T. Kendall has argued that Calvin's view of the atonement differs from that of later Calvinists, especially the Puritans. Kendall interpreted Calvin as believing that Christ died for all people, but intercedes only for the elect.

Kendall's thesis has been disputed by Paul Helm, who argues that "both Calvin and the Puritans taught that Christ died for the elect and intercedes for the elect."

Union with Christ
The believer's mystical union with Christ has an important place in Calvin's theology. According to Alister McGrath, Calvin provided a solution to the Reformation]] problem of how justification relates to sanctification. Calvin suggested that both came out of union with Christ. McGrath notes that while Martin Bucer suggested that justification causes (moral) regeneration, Calvin argued that "both justification and regeneration are the results of the believer's union with Christ through faith."

Predestination
Calvin discusses predestination in his third book of the Institutes. It "does not stand at the beginning of the dogmatic system as it does in Zwingli or Beza", but it "does tend to burst through the soteriological-Christological framework."

In contrast to some other Protestant Reformers, Calvin taught double predestination. Chapter 21 of Book III of the Institutes is called "Of the eternal election, by which God has predestinated some to salvation, and others to destruction".

Sacraments
In common with other Protestant Reformers, Calvin believed that there were only two sacraments, baptism and the Lord's Supper. Calvin also conceded that ordination could also be called a sacrament, but suggested that it was a "special rite for a certain function."

Calvin believed in infant baptism, and devoted a chapter in his Institutes to the subject.

Calvin believed in a real spiritual presence of Christ at the Eucharist. For Calvin, union with Christ was at the heart of the Lord's Supper.

According to Brian Gerrish, there are three different interpretations of the Lord's Supper within non-Lutheran Protestant theology:

Symbolic memorialism, found in Zwingli, which sees the elements merely as a sign pointing to a past event;

Symbolic parallelism, typified by Bullinger, which sees the sign as pointing to “a happening that occurs simultaneously in the present” alongside the sign itself; and,

Symbolic instrumentalism, Calvin's view, which holds that the Eucharist is “a present happening that is actually brought about through the signs.”

Calvin's sacramental theology was criticized by later Reformed writers. Robert L. Dabney, for example, called it “not only incomprehensible but impossible.”