The 26-year-old was taken to hospital on Tuesday after arriving at training complaining of stomach pains.
"Our player Isco has been discharged from hospital," said a statement from the club.
"He will start his recovery process now under the supervision of the Real Madrid medical services."
They did not state how long Isco was expected to be out for, but reports in the Spanish media say the Spain international will be unable to play for around a month and is targeting a return in time for La Liga's October 28 El Clasico against arch-rivals Barcelona.
This would mean he is set to miss a total of six games for Madrid, including a testing midweek league trip to Sevilla and Saturday's derby against Atletico Madrid.
He would also have to sit out UEFA Champions League games against CSKA Moscow and Viktoria Plzen, as well as Spain's friendly against Wales and their UEFA Nations League game with England.
