Although the Three-Fifths Compromise helped Northern and Southern states reach an agreement that allowed for ratification of the Constitution, in the long run it had a negative effect on the nation because

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The negative impact of the Three-fifths Compromise is more inclined to the slave states. In the House of the Representatives,  there was a significant number of legislators that sides the southern parts of the US because some of the laws are for the Southern states. This had lead to the American Civil War.