No one ever asked Mark Twain what his religion was and we are left trying to determine this from his writings and activities. His quotes are presented frequently on atheist quotes sites and much of his writings are aimed at showing the fallacies and faults of organized religion particularly the Christian religion. Many in the "Twain was a Christian" camp indicate that he periodically attended church and was familiar with scripture as "proof". This may have been simply compliance with the customs and social conventions of the time and the frequent use of Christian stories in public speaking.
His family abetted this confusion by hiding his more religion antagonistic writings such as "Letters From the Earth" from the public, leaving them unpublished.
His points on several issues was clear from his writing:
Writing
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Mark twain liked visiting libraries as a youngster.
Mark Twain's first job was as a typesetter.
November 30th 1835
It was Susy Clemens.
Shania Twain
he invented to computer
Susy Clemens, Mark Twains favored daughter.
Elizabeth B Browning
mark twains objestion to impearlism
Samuel Langhorne Clemens