Judge Juan del Olmo of the National Court confirmed indictments he handed down in April against 29 people over the bombings that targeted crowded commuter trains in Madrid on March 11, 2004, killing 191 people and wounding more than 1,800.
Del Olmo rejected appeals from the 29 defendants against those indictments.
He also rejected one from a Spanish prosecutor who wanted to upgrade charges against one suspect from simply belonging to a terrorist organization to taking part directly in the wave of 10 bombs that ripped through the trains.
No trial date was set. This is up to a separate three-judge panel at the National Court, and pretrial motions are expected to take at least several months.
When Del Olmo handed down the indictments in April in a 1,500-page document, he said the Madrid bombing cell was apparently inspired by al-Qaida but had no direct link to it.