But the battle is far from over, judging by the WHO's latest expressions of alarm. It says that in both Nigeria and Afghanistan the number is creeping up, while budget shortfalls are jeopardizing the effort to hold polio at bay in 24 other high-risk countries.
Right now the numbers of new infections are small. But Nigeria's total has jumped to 38 in the first five months of 2012 from just 10 in the same period of last year. Afghanistan's went from three to seven. Only Pakistan's number fell back, from 43 to 18.
The polio virus, which usually infects children in unsanitary conditions, attacks the nerves and can kill or paralyze. It can spread widely and unnoticed before it starts crippling children. On average about one in 200 cases will result in paralysis.
In Pakistan's poor northwest one of the newest victims, 13-month old Fariha, cried out as her 6-year-old sister Sana struggled to place her on the floor, mindful of her tiny legs wrapped in plastic braces.
A laborer's daughter, Fariha was infected six months after birth. She has to be carried everywhere. Twice a day her mother exercises her legs, medicines are provided free and a health worker visits occasionally. The braces were donated by a German clinic.
There are no guarantees that Fariha will fully recover. Most of the new polio cases in Pakistan are in the northwest, where an insurgency rages, making it difficult for health workers to reach tens of thousands of children.
Elsewhere in the world, a growing number of cases are being discovered and traced back to Pakistan and Nigeria. While the numbers are low today, WHO spokesman Oliver Rosenbauer warned that the disease can quickly regain strength. "If a polio-free country becomes re-infected, and the virus gets into an area with low population immunity levels, we have seen time and again that it can take off like wildfire," he told The Associated Press.
Both money and manpower is in short supply and if either runs out before the disease can be eradicated in the three holdouts, an epidemic will follow, says Rosenbauer.
"Polio eradication is at a tipping point between success and failure," he said.
"We have the emergency plans in place through end-2013, and full implementation and financing of the plans could well result in a polio-free world by that time," he said.
Or there could be a worldwide resurgence "and within 10 years we could again see 200,000 cases occur each and every year."
Rosenbauer said WHO's polio eradication campaign needs $2 billion over the next 18 months. So far it is short $940 million, forcing it to cut back programs in 24 high-risk countries.
Every Pakistani and Afghan child under age 5 must be vaccinated several times a year by health workers whose work is often hampered by ignorance, religious extremism, natural disasters and war.
Then there is international travel. "We have seen time and again that polio can spread from these areas to re-infect faraway countries," said Rosenbauer. Between 2009 and 2011, about half of the 3,506 cases worldwide were in previously polio-free countries, he said. Polio was imported into Indonesia for the first time in a decade in 2005 and traced back to Nigeria, and last year, an outbreak in western China originated with a virus from Pakistan.
One problem is Muslim militants who try to block inoculation campaigns by portraying them as a conspiracy to sterilize and reduce the world's Muslim population.
But in Pakistan and Afghanistan clerics and tribal elders have been recruited to support polio vaccinations, opening up areas of the two countries previously inaccessible to health workers.
Shah Mohammed, a WHO worker overseeing vaccinations at a children's hospital in Peshawar, northwest Pakistan, said that of the parents who reject vaccination for their kids, surprisingly few cite religion or the Taliban. Instead they are driven by distrust of their government or of the West's counterinsurgency campaign.
"Many just say: We have no gas, no food, and you come to us with this and nothing else. Why should we bother?" said Mohammed. Or they say "On the one hand the Americans hit us with these drones and on the other hand the Americans are giving us these vaccines. We don't need them."
On Saturday the Taliban in North Waziristan announced a ban on all polio vaccinations until U.S. drone assaults in that area end, effectively ensuring tens of thousands of children under five will not be vaccinated.
A temporary setback was caused by revelations of the CIA ruse to pinpoint Osama bin Laden's whereabouts by collecting DNA from his household under the guise of performing vaccinations.
"The very next (vaccination) campaign there were a lot of refusals," said Dr. Pervez Yousaf, a WHO officer in Islamabad. But it was temporary and restricted to areas around Abbottabad, where bin Laden was killed, he said.
An alliance of U.S.-based NGOs wrote to CIA chief Gen. David Petraeus, warning him against using humanitarian work as a cover for covert operations.
For polio victims in Pakistan and Afghanistan, getting artificial limbs, braces and physiotherapy can be almost impossible, say doctors and health care workers in both countries.
Fifteen-year-old Musa lives in a village in Afghanistan's eastern Paktika province. War rages around it and access for vaccinators is sporadic and difficult. He caught polio at age 3 and went untreated for years.
But he says his five brothers and three sisters have all been vaccinated since. He still needs crutches, but is practicing new ways to move.
And in little Fariha's village of Aziz Khan Garhi, where polio had been unheard of before she was diagnosed, health care workers have vaccinated the entire village and Fariha's grandfather, Yousuf Khan, has led the drive.
"After this all our children have been vaccinated," he said.
Kathy Gannon is AP Special Regional Correspondent for Afghanistan and Pakistan and can be reached at http://www.twitter.com/kathygannon. Geneva Correspondent Frank Jordans and Asia Medical Writer Margie Mason contributed to this report.