http://www.factcheck.org/2016/07/clintons-handling-of-classi...
> More than 2,000 of the 30,490 emails Clinton turned over to the State Department contained classified information, including 110 emails in 52 email chains that contained classified information at the time they were sent or received. (Most emails were retroactively deemed to contain classified information by the U.S. agencies from which the information originated.)
> Some of the emails containing classified information “bore markings indicating the presence of classified information,” contrary to Clinton’s claims that none was marked classified. Comey did not provide a specific number.
> "Only a very small number of the emails containing classified information bore markings indicating the presence of classified information," Comey said. "But even if information is not marked ‘classified’ in an email, participants who know or should know that the subject matter is classified are still obligated to protect it."
It's also entirely possible that of the thousands of emails that were not turned over, some of them contained classified information. We know there were a non-zero number of these:
> Among those several thousand work-related emails that were not provided to the State Department, Comey said, "three of those were classified at the time they were sent or received; one at the secret level and two at the confidential level. There were no additional top secret emails found."