He will have to undergo surgery following a check up and Jordi Roura will take charge of the team in his absence.
Barcelona have made a record breaking start to the season, winning 15 of 16 league games.
A statement from the club read: "During ongoing monitoring, an extension of the pathology has been detected in [Vilanova's] parotid gland. The manager requires surgery which he will undergo this Thursday. He is expected to remain in hospital for three to four days.
"After the surgery, Francesc 'Tito' Vilanova will undergo chemotherapy and radiation treatment for approximately six weeks. During this time, and depending on how well he recovers, Vilanova's treatment may be compatible with his work life. Keeping in line with the patient's wishes, we request respect and privacy during this process."