Because the Cathars were the largest heretical sect to threaten the authority of the Catholic Church in nearly 900 years (since the Manichaeans), Pope Innocent III took the liberty to resolve the Languedoc region of France from the Cathar presence. This crusade is the first and only crusade ever instituted against fellow Christians. Before this crusade was instigated, there was little fighting in the peaceful region of Languedoc, France.

Some powerful nobles and bishops vowed to protect the Cathar leadership, which threatened the Catholic Church even more. These bishops were likely upset with the dominance of papal authority within their sees, and offered to protect the Cathars out of spite. However, in 1204, the Pope suspended the authority of these bishops and excommunicated any nobility associated with the Cathars.

The Cathar Crusade was meant to be a peaceful conversion, but this proved wildly unsuccessful. On July 21, 1209, an army of nearly 30,000 knights and infantrymen poured into the Languedoc region, descending from Northern Europe. Crops were burned, entire towns and populations destroyed. The Holy army held nothing back. Some scholars consider this the first case of genocide in modern European history.

Entire populations were executed at once; some were even inside the church when the army came into town. One young knight asked a papal representative how he would be able to tell the difference between the Catholics and the heretics. The Pope’s representative eerily replied, "Kill them all. God will recognize his own.”. This same papal representative later reported to the Pope “neither age, nor sex, nor status was spared”.

Despite killing many of the Cathars and destroying their towns and homes, some Cathars managed to escape. These few individuals fled to remote hiding places. Upon the conclusion of the Cathar Crusade, the Pope ordered a papal inquisition. This was to be certain that the Cathars were no longer a threat to his authority and the authority of the Roman Catholic Church.