But local health officials say there's no reason to worry.
"This vaccine has followed the same procedure and protocol that every other vaccine has that we have administered for seasonal flu for a long period of time. We follow the exact same procedures. The CDC has gone through the same processes. The FDA has gone through the same processes, so this is a safe vaccine and it's been rigorously tested," said Wake County Community Health Director Sue Lynn Ledford.
People who are suspicious of the new vaccine point to problems with a swine flu vaccine in 1976 - when more people died from the vaccine than they did from the flu.
Natural medicine proponents claim other possible side effects like autoimmune disorders.
"It is one of the most dangerous vaccines ever devised," claimed author and lecturer Dr. Russell L. Blaylock.
But North Carolina State Epidemiologist Dr. Megan Davies says the H1N1 vaccine is manufactured the same way as the regular seasonal flu vaccine - only the strain is different. She calls the seasonal flu vaccine the safest vaccine out there.
"It's so safe I made sure I got the seasonal flu shot when I was pregnant two years ago. People should feel comfortable getting the H1N1 vaccine since it's made the same way, as long as the proper guidelines are followed," she said.
This week, doctors began giving the nasal swab version of the vaccine. The shot version - which will account for the bulk of the doses - is expected in North Carolina next week.
The federal government has ordered some 250 million doses - which it says will mean plenty to go around.