There's an entertaining and instructive website on the legendary Kilroy at http://www.bbc.co.uk/dna/h2g2/alabaster/A414749.
According to this source, the original Kilroy was a riveting inspector in a US shipyard during WW!!; he used the Kilroy drawing and phrase to indicate that he'd carried out an inspection, and they were copied by US servicemen who saw them on the inside of the vessels bringing them to Europe.
No one can really say for sure. The most widely accepted version is that of a shipyard inspector, who after checking on assigned work would scrawl " Kilroy was here". To view other interpretations click here. target=_blank>http://www.kilroywashere.org/001-Pages/01-0KilroyL egends.html">here.