The patents cover technology used in Apple's VPN on Demand software back to 2009, its FaceTime messaging system back to 2010, and its iMessage software.
The trial follows one in 2012 in which Apple was found to infringe on Virnet X patents but managed to overturn the verdict on appeal.
On Wednesday, a jury in the Eastern District of Texas found for VirnetX and against Apple on all counts, going on to find the infringement was willful -- a legal finding that can greatly increase damages.
The Eastern District court is a popular place for patent infringement lawsuits and has earned a reputation as somewhere that favors patent holders in such disputes.
Apple has already asked the judge to declare a mistrial after lawyers for VirnetX made what Apple called "arguments outside the evidence, blatantly misrepresenting the testimony of Apple witnesses."
Those statements "served to confuse, mislead, and inflame the jury, to render a verdict not based on the record."
Both VirnetX and Apple did not respond to requests for comment.
The four patents at the heart of the case were U.S. Patents 6,502,135; 7,490,151; 7,418,504 and 7,921,211.