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The great flood that occurred in Genesis as well as in the story of Gilgamesh has several things in common.  The first way the two stories are similar is in the purpose of the flood.  In both stories, mankind had become intolerable, through evil and babble, and needed to be destroyed.  Another similarity in the two stories is the instruction to build a vessel, either a boat or ark.  The purpose of the vessel was to save a chosen group of people from destruction.  Saving a select group of people is another way the stories are similar.  Both Noah and Utnapishtim were given instructions on how to build the vessel and save their families.  

In contrast, the story in Genesis and Gilgamesh have some differences too.  The most obvious difference is the amount of time that it rained.  In the Bible, it rained for 40 days while in the Epic it only rained for six days.  Another difference I found was in the description of how the boat/ark was set adrift.  For Noah, the boat was built and then picked up by the rising flood waters while Utnapishtim’s boat had to be launched by the shifting of ballasts.  The last difference would be the authors of the stories.  Genesis was written by one, true God while Gilgamesh was 2/3 divine and 1/3 mortal.  

The similarities between these two stories leads me to believe there is some truth to the two stories, regardless if your are religious or not.  In my opinion, there are too many similarities between many stories (Aboriginal, Mesopotamian, Bible, etc) for this event to think that it did not occur.  It is also apparent that the reason for both accounts of the flood is mankind.  The wicked and unworthy ways of humans had to be destroyed.