By April 1793, Whitney had designed and constructed the cotton gin, a machine that automated the separation of cottonseed from the short-staple cotton fiber.the industry was for farming.

Eli Whitney's invention of the cotton gin revolutionized the cotton industry in the United States. Prior to his invention, farming cotton required hundreds of man-hours to separate the cottonseed from the raw cotton fibers. Simple seed-removing devices have been around for centuries, however, Eli Whitney's invention automated the seed separation process. His machine could generate up to fifty pounds of cleaned cotton daily, making cotton production profitable for the southern states.

Farmers throughout Georgia resented having to go to Eli Whitney's cotton gins where they had to pay what they regarded as an exorbitant tax. Instead planters began making their own versions of Eli Whitney's gin and claiming they were "new" inventions. Phineas Miller brought costly suits against the owners of these pirated versions but because of a loophole in the wording of the 1793 patent act, they were unable to win any suits until 1800, when the law was changed.

Whitney, Eli, 1765–1825, American inventor of the cotton gin, b. Westboro, Mass., grad. Yale, 1792. When he was staying as tutor at Mulberry Grove, the plantation of Mrs. Nathanael Greene, Whitney was encouraged by Mrs. Greene and visiting cotton planters to try to find some device by which the fiber of short-staple cotton could be rapidly separated from the seed. Whitney, whose creative mechanical bent had been evident from boyhood, completed his model gin early in 1793, after about 10 days of work, and by April had built an improved one. With Phineas Miller, Mrs. Greene's plantation manager (and later her husband), he formed a partnership to manufacture gins at New Haven. He was unable to make enough gins to meet the demand, and although the partners received a patent in 1794, others copied his model and soon many gins were in use. After much litigation the partners received (1807) a favorable decision to protect their patent, but Congress in 1812 denied Whitney's petition for its renewal. His invention, which had immense economic and social effects, brought great wealth to many others, but little to Whitney himself. In 1798 he built a firearms factory near New Haven. The muskets his workmen made by methods comparable to those of modern mass industrial production were the first to have standardized, interchangeable parts.