What were Martin Luther's main disagreements with the Catholic Church? What were Martin Luther's main disagreements with the Catholic Church? Were these beliefs of Luther's and his disagreements with the Catholic Church the origin of the Lutheran Church?
The Fundamental Change

So the question is: How did Luther change from a Catholic theologian to a Protstant theologian? Or to highlight more the historical aspect: How did he change from a late-scholastic to a reformer? Or a last variation: How did the early Luther change to the "old Luther"? 

This leads us to a certain happening, to a conversion-like radical change in his life. What I'm talking about is the so called tower experience of Luther. 

The Luther before this experience is the Luther of the monastery-struggles. With increasing progress he can not find inner peace – neither by the sacramental means of grace nor by monastic pastoral care. In light of the coming angry justice of God, that he was taught, he despairs.

Now Luther insists on trying to understand what that righteousness is. According to the doctrine of the Catholic Church at that time, this righteousness must be understood as a philosophical, formal and active righteousness. This means: God is righteous and punishes the sinner and unrighteous. Luther not only despairs, but even hates this doctrine. 

In that situation, the above-mentioned tower experience can take place, since Luther discovers, that Romans 1:17, doesn't only say


  For therein is the righteousness of God revealed


But rather has to be read in its context:


  For therein is the righteousness of God revealed from faith to faith: as it is written, The just shall live by faith.


This makes Luther understand: The righteousness of God is this righteousness, which lets the just live by faith through God's gift. According to that Luther builds his understanding of righteousness inspired by Paul: it's passive and makes the sinner righteous by faith and not by any good work. 

This is, what changes Luther from a Catholic theologian to a Protestant theologian.  

From that point on, the Lutheran doctrine starts to grow. 

Against Sale of Indulgence

He starts critisizing the sale of indulgences since they imply that righteousness can be reached by a good human work. According to Luther it can only by reached by faith in God, who makes the sinner righteous.  

Against the Communion as a Sacrifice

For Luther the communion is a promise of God and not a sacrifice, like the Papacy has taught, as he says in his book The Misuse of the Mass (1521):


  Sacrifice and promise are more apart from each other than east and west, rise and decline. A sacrifice is a work, that we give God, whereas the promise is God's word, which gives us God's grace and mercy. It is inconceivable how Gods promise could become a human sacrifice. [...] They give, but Christ promises the people. 
  (WA 8, 512, 12 and 28)


And much more …


Against the Papacy 
Against the free will (See one of his main works "De servo arbitrio")


A final word …

Luther was misused by some European principalities in the 16th century to shrink the popes and the Kaiser's influence. Against Luther's will it came to a schism, building of the Lutheran church and other confessions of Protestantism.