He was in a critical condition after the attack by two armed men who burst into the house in Greenfort Crescent in Clondalkin, west Dublin, shortly before 7.10pm.
He was given Last Rites in hospital last night after he was gunned down at his brother's home in Dublin.
The convicted drugs trafficker is expected to make a recovery after undergoing surgery overnight.
Earlier this afternoon, his wife Geraldine, brother Thomas and daughter Tracey were spotted leaving the hospital.
Gilligan's family and friends stayed at the hospital overnight as they awaited word of his condition.
Gilligan had just stopped off in the house after attending a Christening party at a pub.
According to sources, Gilligan was shot seven times as he sought refuge in the toilet, and sustained injuries to his face, chest, hip and leg.
He was shot once in the chest – but the bullet missed his heart and lungs.
A source said he was shot once in the face, which "took a chunk out of the forehead".
Gilligan was shot in the hip, and it's believed the bullet may have travelled into the stomach. He was also shot in the leg. A source said: "His eyes were full of blood."
Gilligan – who gardai believe ordered the murder of Sunday Independent journalist Veronica Guerin – fell to the ground bleeding as the gunmen fled from the scene.
Paramedics received a call from family members. A voice on the line said: "It's John Gilligan – he's been hit."
Earlier reports from the scene had suggested he was wearing a bullet proof vest, but it is now understood that he was not at the time.
Despite the multiple shots, he was still conscious as he was rushed to hospital by ambulance.
The critically injured gangster arrived at Connolly Hospital, Blanchardstown at 7.36pm where he was met by chaplain, Fr Dan Joe O'Mahony, who administered the Last Rites, said to be "standard procedure" after such a serious shooting incident.
Sources last night described how several gardai were in attendance in the Emergency Unit as medical personnel fought to save his life. He was said to be "conscious" at all times but unresponsive.
"He was aware, but out of it – if that makes sense," one source said.
Sources said Gilligan was shot shortly after he got a lift to his brother's house from his daughter, Tracey.
Gardai were still trying to establish his movements yesterday but sources said he may have spent the day at Jessbrook equestrian centre in Kildare, and travelled to Dublin for the Christening party in a Palmerstown pub.
His daughter dropped him off at the house some time before 7pm. She remained "in the vicinity" outside, according to sources, and may have planned to take her father on to the party in Palmerstown.
It was unclear last night whether anyone else was in the house at the time of the shooting.
But according to Garda sources, there were "very very few people" there.
Detectives were last night trying to retrace Gilligan's movements in an attempt to find out whether the gunmen had followed him.
Last night's shooting follows a number of threats on Gilligan's life since his release from prison last October.
Gardai said Gilligan had been under close surveillance by criminal rivals in recent weeks. But despite receiving numerous warnings of serious threats to his life, Gilligan refused to co-operate.
He was shot at the same house where he was welcomed with party masks and beer on his release from prison.
It was the second attempt on his life in two months. On December 14 last Gilligan narrowly avoided death when assassins went to the wrong north Dublin pub.
The attempts on Gilligan's life arise from a contract put up by other major drug traffickers who were forced to flee the country in the wake of Veronica Guerin's murder.
Gardai believe a hired assassin, understood to be from north inner Dublin, was contracted to kill Gilligan in December. However, there was no indication of who was behind last night's attack.