The activity comes as President Obama declares the swine flu outbreak a national emergency. The White House says Mr. Obama signed the proclamation Friday night.
Officials said the move is similar to a declaration ahead of a hurricane making landfall.
Swine flu is now more widespread than it's ever been.
The declaration empowers Health and Human Services Secretary Kathleen Sebelius to bypass federal rules so health officials can respond more quickly. That could mean fewer hurdles involving Medicare, Medicaid or health privacy regulations.
The H1N1 outbreak has resulted in more than 1,000 deaths in the United States. Almost 100 of them are children, and 46 states now have widespread flu activity.
Municipalities have been dependent on drug companies for their supply of the vaccine, and production has been slower than expected. There have been several other H1N1 inoculation clinics in the Chicago area over the last week, but Saturday was the first one in the city. And there was a big response.
The lines stretched out the door. Chicago residents came from all over the city, hoping they could get someone to stick a needle in their arms or a spray up their noses. Those in line believed that was a minor inconvenience compared to coming down with the H1N1 virus.
"Even if it does a little bit of pain or discomfort, it's better than the other possible outcome," said Nick Goga, 19.
Health care workers called them up by numbers, and many had waited an hour or more. But for those among the chosen, after filling out some paperwork, they got the shot they hope will prevent them from getting the virus.
Despite polls that show a high percentage of people plan to avoid the vaccine, those in line in Chicago believed in it.
" I want to know I'm healthy and I'm not vulnerable to something that might be detrimental to me," said 58-year-old Lynda Ebhardt.
"I just want to make sure I got it so I don't get sick, I guess, because everybody is saying how bad it is -- as a precaution," said Eddie Taylor, Chicago resident.
The Chicago Department of Public Health offered seven clinics in various neighborhoods. Each clinic had about 1,000 doses of the vaccine available and at each location they used it all up and had to turn some people away.
"If we had more supply, we could give it to more people, but we don't. So, we are limited by that," said Dr. Terry Mason, Chicago health commissioner.
A White House statement reads, "We have taken proactive steps to reduce the impact of the pandemic and protect the health of our citizens."
But it will do little to speed up delivery of the vaccine.
"vaccination is our strongest tool and not having enough of it is extremely frustrating," said Dr. Thomas Frieden of the Centers for Disease Control.
The city expects more doses of the vaccine in time for more clinics like this planned for later during the week. They are trying to serve high-risk residents first, including pregnant women, children, and those with pre-existing conditions. They suggest those who have insurance get the shot from their doctor. But that can be a problem, too.
"The pediatricians don't have the vaccine yet. So, I tried to get out here early so we could get her vaccinated before the flu hits worse than it already is," said Chicago resident Charlene Wiegand.
The city clinics are planned for Tuesday and Thursday from 3 p.m. to 8 p.m. The health commissioner, Dr. Mason, says he expects enough shipments to be able to keep that schedule.
He says the city will continue to offer the clinics three times a week until everyone who needs the vaccine gets it.
Chicago's vaccine info:
Chicago Health officials expect to administer 30,000 doses a week at three colleges in the city:
Those vaccines will be given out Saturday from 9 a.m. to 2 p.m. and Tuesdays and Thursdays between 3 p.m. and 8 p.m. on a first come, first serve basis. Locations/Times Free Vaccines offered in Chicago (PDF).
"In Chicago people are concerned. They're concerned mostly because of how it affects children. And I can understand that. Now, we don't want everybody to show up because we can't give that to everybody in one day. There will be plenty of vaccine. He'll be giving vaccine almost every week," said Dr. Terry Mason, Comm. Chicago Health Dept.
Because of limited supplies, Chicago Department of Health Commissioner Doctor Terry Mason and all health officials say until more doses come in, vaccines are reserved for:
Officials warn people who are allergic to eggs should not get a vaccine.
"Is it safe? Well, it's being made the same way we make all the other vaccines. And part of the reason why it's taking a little longer is because the process of production requires some very rigorous testing," said Mason.
DuPage County vaccine info:
Beginning today, the DuPage County Health Department is offering free doses of the vaccine at its central office. The clinic will be open from 4-8 p.m. on weekdays and 7 a.m.-3 p.m. on weekends through November 8. Times will expand next week as more vaccine arrives. In coming days, they will have appointments available at satellite offices. The time slots are already booking up. Schedule of vaccine clinics in DuPage County
County health staff prepared an elaborate system for greeting, screening and vaccinating residents against the H1N1 virus. There are 10,000 doses of both the nasal and injectable forms of the vaccine on hand. On Thursday, 350 will be used up on those who have been persistent enough to get an appointment.
"My wife spent about 35 minutes on the phone last night. I think she took 15 minutes to get through and 20 minutes waiting on the line," said Bill Childress, father.
"We want to have control over crowd control and be able to get the vaccine to the people who need it first," said Maureen McHugh, executive director, DuPage County Health Department.
McHugh believes as the clinics intensify efforts, people's misgivings about getting the H1N1 vaccine will fade. They'll see their friends and neighbors coming in and experiencing minor if any complications from either the mist or the shot.
"Whenever something new hits the horizon, people are a little skeptical. As they see people get the vaccine and respond to the vaccine positively and have really no negative outcomes, I think confidence will grow," said McHugh.
The state's chief of public health, Dr. Damn Arnold, is adamant the vaccine is safe. And those who don't choose to get it are playing a dangerous game with their own health and that of their loved ones.
"The benefit to me is so far outweighing any potential risk," said Dr. Arnold.
Lake County, Ind. vaccines
Health officials in Lake County, Ind., are also offering the H1N1 flu vaccine.
It is being given out Mondays through Fridays from 9 a.m. to 4 p.m. and on Saturdays from 9 a.m. to 3 p.m. at the government complex administration building on main street in Crown Point. For details, call (888) 416-1284. Schedule of vaccine clinics in Lake County