On Friday, Boston Children's Hospital was following the guidelines issued by the Centers for Disease Control and Prevention and reserving scarce vaccine for people age 65 and over, children age 6 to 24 months, women more than three-months pregnant and those with underlying health problems.
Mildred Medina got shots for her three sons, age 9 to 16, because they have asthma.
"I was very concerned. I called my doctor and she said to bring them in," said Medina.
But when the flu vaccine runs short, as it suddenly did this year, how is it rationed?
According to Dr. Anthony Fauci of the National Institutes of Health, "You have to be open and transparent and honest about the reasons for the kind of guidelines that you have."
The groups who are supposed to receive the vaccine now are the ones most likely to die from complications of the flu.
"In a context like this when we are trying to prevent deaths, that's the public health goal, really I think the only morally defensible position is need -- who needs the vaccine the most," said Dr. Ruth Faden of Johns Hopkins Bioethics Institute.
But the CDC only has the power to make recommendations.
Dr. Lewis Goldfrank, who heads the emergency room at Bellevue Hospital in New York, says he just can't ensure everyone who needs a shot will get one. "We're down to very few vials and very few doses," said Goldfrank.
How does he decide who will receive a shot?
"We have to use the doses when we've got the people. We have lots of people at risk and they have children or parents and relatives or people who were placed at risk if they weren't vaccinated. So we give it to the people who come through the door," said Goldfrank.
It is clear that even with the new guidelines, tens of millions of people who fall into the high-risk categories will not be vaccinated this year.
Robert Bazell is NBC's chief medical correspondent.