The application was submitted in late December, Merck spokeswoman Amy Rose said Tuesday.
It was long planned as part of Whitehouse Station, N.J.-based Merck's strategy to increase the market for Gardasil. It prevents infection with the sexually transmitted virus and thus cancers of the genital organs.
Gardasil, launched in 2006 for girls and young women, quickly became one of Merck's top-selling vaccines, thanks to aggressive marketing and attempts to get states to require girls to get the vaccine as a requirement for school attendance.
However, it is one of the priciest vaccines on the market, typically costing $360 for a three-dose regimen.
Gardasil had 2007 sales of $1.5 billion, but sales began slowing in the second half of 2008, after a government-funded Harvard study concluded it was cost-effective for girls but not for women in their 20s.
The U.S. Food and Drug Administration has two months to decide whether the application for use in males meets its standards. Reviews can then take 10 months or more.
The application includes research data from a Merck study including about 4,000 males, ages 16 to 26; Gardasil prevented 90 percent of cases of penile cancer and genital warts caused by the four common virus strains targeted by the vaccine.
The agency approved use of Gardasil in females ages 9 to 26 years old in June 2006, but last June rejected expanding that to include women ages 27 to 45. The vaccine has since been approved for use by young women in dozens of foreign countries.
A rival vaccine called Cervarix, made by Britain's GlaxoSmithKline, is approved in many foreign markets, but generally lags behind Gardasil in sales. It is still awaiting approval in this country.