In March 2013, an adviser to Clinton, Sidney Blumenthal, had his e-mail hacked by "Guccifer" -- the Romanian hacker perhaps best known for revealing George W. Bush's paintings to the world. At the time, Gawker reported that Blumenthal was communicating with an account that appeared to belong to Clinton at the "clintonemail.com" domain. The content of some of those e-mails was published by RT.com.
Examining the registry information for "clintonemail.com" reveals that the domain was first created on Jan. 13, 2009 -- one week before President Obama was sworn into office, and the same day that Clinton's confirmation hearings began before the Senate.
As the Times notes, others have used private e-mail accounts for official business, including former EPA administrator Lisa Jackson. The extent of Clinton's hidden communication, part of her work in a much more significant capacity, is unknown.