He completed the Mark I in 1944. The Mark I was different from Bush's differential analyzer, because it could solve almost all mathematical problems. (Bush's machine only solved differential equations.) Mark I was important, since it was available to people outside of the government. Mark I was electromechanical rather than electronic.

At the Computation Laboratory, Aiken completed new work/findings in mathematical linguistics, the automatic translation of languages, switching theory, and the use of magnetic cores and drums as computer components. He served as Editor of Annals of the Computation Laboratory.

He began construction on the Mark II for the Dahlgreen Proving Ground of the Navy's Bureau of Ordnance in 1945. Unlike the Mark I, the Mark II was built with electromagnetic parts. The construction of Mark III completed in 1950 and was called the Aiken Dahlgreen Electronic Computer (ADEC). The Mark IV was completed in 1952 for the US Air Force. Aiken also helped create a computer science program as well as a computing center at University of Miami. He founded Howard Aiken Industries Inc., a New York consulting firm.