Shkreli, 34, was accused of funneling money from MSMB Capital and MSMB Healthcare investors to Retrophin, and prosecutors argued he then used money from Retrophin to pay them back.
Deliberations on the eight counts against him began on Monday and lasted approximately 36 hours total.
He was found guilty of: securities fraud in connection with MSMB Capital, securities fraud in connection with MSMB Healthcare and conspiracy to commit securities fraud in connection with Retrophin.
He was found not guilty of: conspiracy to commit securities fraud in connection with MSMB Capital, conspiracy to commit wire fraud in connection with MSMB Capital, conspiracy to commit securities fraud in connection with MSMB Healthcare, conspiracy to commit wire fraud in connection with MSMB Healthcare and conspiracy to commit wire fraud in connection with Retrophin.
When the judge announced the verdict, Shkreli appeared to have a serious look on his face as he bowed his head, a departure from the usual smirk he sported throughout the trial. Shkreli's father was also present for the reading of the verdict.
After the verdict, Shkreli walked out from court with a smile and declared himself delighted.
"This was a witch hunt of epic proportions, and maybe they found one or two broomsticks, but at the end of the day we have been acquitted of the most important charges," Shkreli told reporters.
Shkreli’s defense attorney Benjamin Brafman told reporters that five not-guilty verdicts are still a positive, and said he thinks that the three guilty verdicts -- if they survive post-trial motions –- will lead to a lenient sentence.
Bridget Rohde, acting U.S. attorney for the Eastern District of New York, said the prosecution is pleased with the close attention the jury paid to the evidence and feels justice has been served.
Rohde added that the work is not done as Shkreli remains to be sentenced and a co-defendant is also set to be tried in this case.
"As the jury found today, Martin Shkreli violated the law by deceiving investors into entrusting their money with his hedge funds and lying to them about the funds’ performance, as well as by engaging in a multi-million dollar fraud scheme involving publicly traded Retrophin," Rohde said in a Department of Justice press release. "Together with our partners at the FBI, we remain steadfast in our commitment to protecting the investing public and our markets from such fraud and abuse and will continue to hold accountable those who defraud the market."
Shkreli faces up to 20 years when he is sentenced at a later date.
In closing arguments, Assistant U.S. Attorney Jacquelyn Kasulis called Shkreli "calculating."
“Lying to people to get them to invest with you is fraud,” said the prosecutor. ”He knowingly lied over and over again to his investors to get their money and then to keep their money.”
"Who he really is is a con man who stole millions of dollars," she said. Kasulis gave a bank robbery analogy to the jury, arguing that if you rob a bank and then rob a second bank to pay the first bank back, you still robbed a bank. "You can’t rob Peter to pay Paul. It doesn’t work that way," she said. "It doesn’t matter if you paid people back years later after you’ve stolen their money and you’ve lost all their money. Those people are still victims of fraud." Kasulis emphatically stated that Shkreli is not above the law.
"It’s time for Martin Shkreli to be held accountable for his behavior, for his choices to lie and to deceive and to steal and to take peoples’ money without a second thought, without even a pause,” said Kasulis.
Brafman told the jury the alleged defrauded investors ended up making profits because of Shkreli despite their accusations.
Brafman said in this case "Reasonable doubt is now circling the atmosphere like a bunch of drones.”
Shkreli made headlines in 2015 for raising the price of Daraprim, an antiparasitic drug used to treat infections, from $13.50 to $750 a tablet after acquiring the drug from another pharmaceutical company.
Days later, Shkreli told ABC News that the company would lower the price of Daraprim "to a point that is more affordable and is able to allow the company to make a profit, but a very small profit."
After the verdict was announced, Shkreli said in a livestream posted to YouTube that Daraprim costs a “fraction” of other similar drugs and was at risk of disappearing before he acquired it.
ABC News' Julia Jacobo and Dom Proto contributed to this report.