In the 1960s and 70s, the spirits of scores of convicted Japanese war criminals were "enshrined" there.
The most controversial were the 14 "Class A" war criminals, including wartime leader Hideki Tojo, who were "enshrined" in the late 1970s.
These men were the ones who ordered and oversaw Japan's brutal war in China and South East Asia.
Yasukuni Shrine
It was a war in which millions died, in which there were widespread massacres of civilians, in which rape was routinely used as a weapon and where Japan used chemical and biological warfare against civilians.
So if the shrine is so offensive to China and South Korea why did Mr Abe go?
Firstly, because he wanted to.
Close observers of the Japanese prime minister say he is at heart a nationalist and a historical revisionist.
He believes the trials that convicted Japan's wartime leaders were "victors' justice".
His own grandfather Nobusuke Kishi served in the war cabinet and was arrested by the Americans on suspicion of being a Class A war criminal. He was later released without charge.
But the stain of association with Japan's war crimes in China never completely went away.
Secondly, Mr Abe's support base comes from the right wing of the Liberal Democratic Party.
According to Professor Jeff Kingston of Temple University in Tokyo, Mr Abe is "showing he is a tough guy", that he is not afraid of China. It is something that plays very well to his base.
But there is perhaps a bigger goal that Mr Abe has in mind.
He wants to radically revise Japan's post-war constitution.
This, too, is a long-held dream that started with his grandfather in the 1950s.
Mr Abe believes he is the man to complete the historic task of getting rid of the hated "peace constitution".
Like many on the right here, Mr Abe believes that constitution was forced on Japan by America and is a humiliation.
It imposes not only pacifism, but also Western notions of human rights and civil liberties. It rejects Japan's uniqueness in favour of "universal values".
Mr Abe would like to change a lot of this. But it will be very hard. And so he will need some help.
"Abe has provoked China, and China has reacted just as Abe wanted it to," says Prof Kingston. "There is a shrewd political calculus at work here."
What he means is that having an external threat in the shape of big and frightening China may be just what Mr Abe wants to help push through his controversial nationalist agenda at home.

About 110 boats, including civilian vessels, took part in the search for Paul Ormsby and Ciarán Smith.
The co-ordinated search took place along the Irish west coast on Saturday.
Both men have been missing since Irish Coast Guard helicopter Rescue 116 crashed off on 14 March.
Four people were on board the helicopter when it came down off the County Mayo coast.
Capt Dara Fitzpatrick died after she was rescued from the sea hours after the crash.
The body of her co-pilot, Capt Mark Duffy, was later recovered from the wreckage.
Last Sunday, the wreckage of the helicopter was lifted from where it crashed near Blackrock Island but the two missing crew members were not found.
Saturday's search involved the Irish Coast Guard, RNLI, Irish Air Corps, Irish Naval Service and Irish Civil Defence, along with more than 80 civilian boats.
However, the extensive search, which stretched over hundreds of square miles from County Donegal to County Mayo, failed to find any sign of the two men.
Inshore boats worked close to the coastline and larger vessels further out to sea.
Helicopters searched from the air while a shoreline effort was assisted by search and rescue volunteers from across the Republic and Northern Ireland.
Search teams from Counties Down, Wicklow, Dublin, Donegal, Claire and Tipperary were among those who took part.
The search came days after an appeal from a sister of Ciarán Smith for help from fishermen and coastal communities in searching for the men.
Speaking after the search, Orla Smith said the support show by the fishing communities had given the families renewed hope and that there were no words to thank those involved in the search.
An investigation into what happened to the helicopter is continuing.
The Air Accident Investigation Unit has said there was no indication of any mechanical problems in the seconds before the impact.
It is thought the inquiry into the cause of the crash on 14 March will now focus on operational issues.
Whatever Shinzo Abe says, any visit to the Yasakuni shrine by a Japanese prime minister is deeply political and sure to cause offence.
[NEXT_CONCEPT]
A major sea search described as one of the biggest in Irish state history has failed to locate two Irish Coast Guard crew members missing since a helicopter crash.