He is accused of fraud relating to a drug company he previously headed, Retrophin, and a hedge fund, where he was a manager.
He denies the charges but faces up to 20 years in prison if convicted.
Mr Shkreli, 34, made headlines in 2015 when his firm raised the price of Daraprim, used by many Aids patients, from $13.50 per pill to $750.
That controversy is unrelated to the fraud trial.
Prosecutors accuse Mr Shkreli of running a fraudulent scheme where Retrophin assets were used to pay off debts after hedge fund MSMB Capital Management lost millions of dollars.
They allege that he cheated investors out of $11m (Â£8.6m).
Mr Shkreli was head of Turing Pharmaceuticals when the price hike of Daraprim occurred.
In a storm of media coverage, he was branded "the most hated man in America" and dubbed "Pharma bro", but he defended the price increase saying the drug was highly specialised.
He stepped down as head of Turing in 2015 following his arrest on the fraud charges. He has been free on bail pending the trial.
Daraprim treats toxoplasmosis, a parasitic affliction that affects people with compromised immune systems, and is used by Aids patients.
Former pharmaceutical chief executive Martin Shkreli has gone on trial in New York charged with fraud.