NEW YORK (CNNMoney.com) -- Apple is investigating the timing of stock options granted to some employees, including one made to CEO Steve Jobs, the Cupertino, Calif.-based maker of iPods and Mac computers said Thursday.

Apple (Charts) said its internal investigation has discovered irregularities related to grants issued between 1997 and 2001, including one made to Jobs. The company said that grant was subsequently cancelled and resulted in no financial gain for Jobs.

Apple said a special committee of outside directors has hired independent counsel to conduct an investigation, and the company has informed the SEC. Apple will not comment further on the matter until an independent investigation is concluded.

"Apple is a quality company, and we are proactively and transparently disclosing what we have discovered to the SEC," said Jobs in a statement. "We are focused on resolving these issues as quickly as possible."

Shares of Apple fell 3 percent in after-hours trading.

Questions over executive stock options have sparked federal investigations of dozens of companies, many of them technology firms.

The SEC and prosecutors are investigating whether companies "back-dated" stock options for some employees, or retroactively changed the date an options grant was effective, to a date that led to a bigger windfall for those who held the options.

Stock options give executives and employees the right to buy shares at a certain price, and if the stock rises after the options are granted, profits can be fat.

A number of executives have been fired, others have resigned, and some firms are looking at restating financial results going back several years.

The practice of back-dating largely ceased in 2002, when Sarbanes-Oxley legislation took effect and made back-dating harder to do.