In documents posted online, the FDA said the vaccine prevented genital warts in males 90 percent of the time.
The vaccine works by blocking the two strains of the human papilloma virus, or HPV, which causes irregular growths and rare types of cancer in male genitals.
Merck has asked the FDA to approve Gardasil for boys and men ages 9 to 26.
A panel of vaccine advisers will weigh in on the new use next week. The FDA is not required to follow the group's advice, though it usually does.
A 4,000-patient study conducted by Merck compared patients taking Gardasil to patients taking a sham treatment for three years.
Merck had originally asked the FDA to approve the vaccine for prevention of both genital warts and precancerous growths on the penis and anus. However, reviewers said the number of those growths was too small to evaluate.
The Whitehouse Station, N.J.-based company and the FDA agreed to "evaluate a less broad indication focusing only on genital warts," the FDA documents state.