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And the disciples asked him, saying, "Why then do the scribes say that Elijah must come first?" But he answered them and said, "Elijah indeed is to come and will restore all things. But I say to you that Elijah has come already, and they did not know him, but did to him whatever they wished. So also shall the Son of Man suffer at their hand." Then the disciples understood that he had spoken of John the Baptist." (Matt. 17:10-13)
To understand how the concept of reincarnation lost favor in Christian tradition, we must look to the development of the Roman Catholic Church and its doctrines. The first 300 years after Jesus' death, there were many variations of Christian doctrine as the new religion spread throughout the Roman Empire. Some factions believed in reincarnation, some did not. All of the factions were in conflict. In an attempt to consolidate his crumbling Roman Empire, the Emperor Constantine in 325 A.D. offered his official support to Christians if they would settle their differences and establish a unified set of beliefs. The resulting Council of Nicaea put together the foundation of the Roman Catholic Church and established a new doctrine, from which reincarnation was omitted. Christians were instructed to drop any belief that was not covered in the new doctrine.
However, the belief in reincarnation did not disappear easily, and in fact persisted for centuries afterwards. During the early 13th century, the Pope launched a crusade against the Cathars, a Reincarnationist Christian sect in Italy and Southern France, and wiped them out completely. The next blow to the Doctrine of Reincarnation was during the Spanish Inquisition. At this time, there was a fatal intolerance for any deviance from strict church doctrine. This was the final blow in forcing Christians to give up their belief in reincarnation - at least publicly.
Why did the early church care if Christians believed in Reincarnation? Reincarnation undermined the authority and power of the developing church. A believer in reincarnation assumes greater personal responsibility for his own spiritual evolution, relying less on the influence and control of priests, confessionals, and rituals to ward off eternal damnation. None of these trappings of the church were part of Jesus' original teachings, they were added by the men who shaped the original movement .
Early Christianity was subject to the same pitfalls many grass-roots movements face when their original leaders are gone. Of necessity, the followers begin to establish a structure and organization to carry on what was given to them. In the process, some valuable elements can be lost and even replaced by dogma that has more to do with practical concerns (like church finances) than spiritual ideals. Reincarnation has never been in conflict with the tenets of Christ's teachings, merely in conflict with the control wielded by the church.