Prosecutors in New York claim the billionaire used inside information to profit from trading in shares in major technology companies.
A total of 21 people have been charged with offences relating to the alleged arrangement, but only Mr Rajaratnam and Danielle Chiesi, a former employee of New Castle Funds, have been indicted so far.
The pair appeared in court in Manhattan on Monday and both entered not guilty pleas.
US Attorney Joshua Klein asked for a trial date to be set for June or July, before civil action by the Securities and Exchange Commission is scheduled to get underway in August.
However, judge Richard Holwell said he was not prepared to set a firm date for the case at this point.
Mr Rajaratnam is the highest profile figure to be caught up in what prosecutors have described as the most serious hedge fund insider trading case of all time - partly because of his alleged links to the Tamil Tigers terrorist group.
Others arrested in connection with the investigation include ex-executives from Intel and McKinsey & Co, as well as Robert Moffat, who left his position as senior vice-president at IBM after being charged with passing on information.
By Tony Aynsley