For example, employees using their own encryption programs, unsanctioned by the enterprise, can still encrypt documents before sending them out to cloud storage, to file sharing sites, to their personal email accounts, or to untrustworthy third parties.
And malware programs that use encryption to hide malicious traffic aren't likely to share keys with enterprise firewalls.
But even if this traffic can't be decrypted, the very existence of unsanctioned encrypted traffic is a warning sign, said Bryan Simon, SANS Certified Instructor at SANS Institute and president and CEO of Xploit Security.
"The proxy knows when it can't read the traffic," he said. "That's an indicator of a bad connection."
In addition, malware might not even know that it's supposed to go through the proxy, he added.
"If you have continuous networking monitoring in your environment, you can tell if your clients are launching legitimate SSL connections versus malware," he said.
Of course, malware writers will adapt, he added.
"The adversary will use what they can," he said. "If they can't do encryption, they'll go plain text. They don't care. They're that brazen."
Monitor traffic destinations — and origins
Another approach for handling encrypted traffic is to look for suspicious destinations, said Jason Lewis, chief collection and intelligence officer at Lookingglass.
"The attacker still needs to move the data out of the enterprise and they commonly use known malicious infrastructure as the destination," he said. "If the security team is unable to look inside the traffic, they can still observe where the traffic is going."
In addition to known malicious sites, enterprises can also look for other signs that the traffic isn't legitimate.
"For example, if encrypted traffic is headed to the Tor network, it's an easy decision to disallow that communication," he said.
Companies can also look at where the traffic is coming from. Not all enterprise systems need to be communicating with the outside world, said Jean-Philippe Taggart, senior security researcher at Malwarebytes Labs.
"Sometimes it isn't about if the traffic is encrypted, but if there should be any traffic emanating at all," he said.
The amount of data being transferred can also be a clue, said Muddu Sudhakar, co-founder and CEO at security firm Caspida.
"A large amount of data transferred to an unfamiliar IP address is potential threat indicator," he said.
Be ware of privacy concerns
When employees have an expectation of privacy when it comes to, say, their personal use of the Internet while at work, then a warning from the IT department that they're violating corporate communication policies can be an unwelcome shock.
"CSOs should communicate clearly with the staff that their traffic is actively monitored," said Malwarebytes' Taggart.
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