But five of Rowan County Clerk Kim Davis' six deputies later told the judge in a second hearing that they were willing to issue the licenses.
Davis, who broke down crying, was led away by U.S. Marshals after the first hearing.
The 49-year-old woman, who has emerged as a darling of social conservatives, has refused to issue licenses to any couples, gay or straight, since the U.S. Supreme Court in June ruled that same-sex couples have the right to marry under the U.S. Constitution, citing her beliefs as an Apostolic Christian.
Thursday's proceedings were the culmination of months of legal wrangling and refusals to abide a judge's order to do her job that had drawn national attention from those both for and against gay marriage rights.
"Marriage is a union between one man and one woman," she told the court under questioning by her attorney.