The 44-year-old has suffered a relapse of a cancerous tumour he had removed from his parotid gland in emergency surgery last November.
“While monitoring his parotid gland a change has been detected in his condition that requires surgery,” a Barcelona statement said.
“The time of hospitalisation is expected to be three or four days.”
The statement added: “According to how things develop, he could be able to mix work with his treatment.
“Keeping in line with the patient’s wishes, we urge respect and privacy during this process.”
Vilanova, whose Barcelona side are currently nine points clear at the top of the Spanish league, took over from Pep Guardiola in the summer.
Club president Sandro Rosell cancelled a news conference scheduled for Wednesday, and the Catalan side also called off their Christmas lunch organised for the media.
• Vilanova began his footballing career in Barcelona’s youth section, joining La Masia in 1984 and sharing a dressing room with the likes of Albert Ferrer, Guillermo Amor, Carles Busquets and Josep Guardiola, whom he would later assist and succeed as coach of the Blaugrana.
• He only made three friendly appearances for Barcelona’s senior side in 1988-89, dropping down to the second tier for three seasons before eventually reaching the top flight with Celta Vigo.
• He began his coaching career with Barcelona’s Cadet B team, working with Gerard Piqué, Cesc Fàbregas and Lionel Messi.
• Vilanova was then asked by Guardiola to join him as an assistant with Barça’s B team and together they helped earn promotion to Spanish third division. Shortly afterwards Vilanova joined his former team-mate in the senior set-up, where he would go on to share in 14 trophies over a four-year period.
• Following Guardiola’s resignation in summer 2012, he was promoted to head coach and began his reign in style with a 5-1 Liga defeat of Real Sociedad de Fútbol.
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