The historic complex, where 1.2 million immigrants received medical care between 1901 to 1954, has opened to to the public for the first time in 60 years.
Many immigrants were sick after long boat journeys and needed immediate treatment within its walls. All arrivals needed to be medically cleared before they were granted permission to stay in the U.S.
"Often they would have come into this building and be examined," said Antoni Mrozinski, a volunteer with Save Ellis Island. "They first would have checked for lice. If they had lice, their head was shaved. It was an easy cure."
The complex of 29 un-restored buildings is located across the ferry slip from the fully-restored Immigration Museum. As part of the tour opening, an art exhibit, "Unframed - Ellis Island," by artist JR will be on display.
The exhibit uses life-size historic photographs of Ellis Island immigrants tucked in throughout 22 interior walls.
"Their clothes would have been taken... washed and sterilised," Mrozinski explains. "They would have received a bath. They would have been washed down. Remember, most of these people had spent a minimum of two weeks in steerage. They were a little dirty and a little smelly."
The tour includes the autoclave - an early sterilisation room where equipment and bedding were subjected to high-pressures and steam.
In its day, the complex was the largest Public Health Service institution in the United States.
Sick and pregnant immigrants were treated and cured before they were allowed to enter the country - or were sent back to their native land.
About 3,500 people died at Ellis Island - of which 1,400 were children felled by scarlet fever, tuberculosis and other illnesses rampant in those years.
Jessica Cameron-Bush, director of education at Save Ellis Island explains that prospects were not good for those that arrived without the means to pay for treatment.
"If you showed up here sick and you were admitted to the hospital, you had to either appeal, your family could say that they could pay for your treatment, the doctors would say, "this is what they have, this is how long it will take to treat them and this is how much it will cost," and your family had to prove that they could pay for you. Then you could be treated, then you could be admitted," she said.
If friends or relatives were not able to pay or if the patient had a disease that could not be cured then they would not be admitted. Instead they were sent back home on the next available ship - an unpleasant prospect for those arriving in America hoping for a fresh start in life.
"If you found yourself in this room, you were pretty bad off," Cameron-Bush said. "For most people this was your last stop on Ellis Island. If you couldn't be made better here, you either died or you were sent back to your home country. So your last view out that window is the Statue of Liberty."
In an age before antibiotics the only way to treat people with tuberculosis was to quarantine them, many of the separate rooms can be visited on the tour.
The hospital was built using pavilion architecture, made popular after Florence Nightingale's observations during the Crimean War that more people were getting sick in hospital than out, because of the rapid spread of infection.
Visitors on the tour will need to don hard hats, and could be wandering through broken glass into rooms without electricity and across overgrown grass strewn with refuse.
But these won't be the first visitors to Ellis Island's hospital wards. It sounds gruesome, but doctors from across the US arrived here to watch autopsies because they could learn about strange and unusual diseases from distant parts of the world.
The areas where the public will go on the tour have been tested (for air quality) and cleaned, but nothing has been restored.
The 90-minute tours will take place four times a day and will be limited to 10 people per tour.
Proceeds will go toward the continued preservation and restoration of the complex.
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