When Stacey Mathias-Geer's son starts his first day of junior kindergarten this week, among the child-sized backpacks, spanking new coloured markers, excited giggles and anxious tears, there will be one thing the four-year-old won't share with most of his classmates - a vaccination record.

Mathias-Geer and her husband, who have a small farm near Sudbury, Ont., have chosen not to have Satya and his nine-month-old brother Darshan inoculated with the vast array of vaccines recommended for children.

Although immunization is mandatory before children can attend school in Canada, parents can obtain an exemption based on a number of criteria, including religion and reasons of conscience.

"It's not a decision I made lightly," says Mathias-Geer, 32, a freelance journalist who has studied much of the medical literature on vaccination.

"My big concern, and sort of the holistic concern, is that you're not only dealing with chemicals and biological materials, but you're bypassing the main part of the immune system to do it," because the injections go into muscle and directly into the bloodstream, she says.

"Some studies suggest that can have an impact on the immune system, which may lead to autoimmune disorders" such as allergies, asthma, rheumatoid arthritis and multiple sclerosis, caused when the body's disease-fighting cells turn on healthy tissue, she adds.

"In other words, you're monkeying around with the immune system, in my opinion, without knowing enough about it to be doing it . . . To me, when I really looked at the long-term research that's out there - it's not good enough. Not good enough to convince me that I should be vaccinating my children."

Parents often worry about the effects of vaccines on the immune system, especially since several can be included in a single injection, says Dr. Michelle Ponti, a London, Ont., pediatrician.

"But the fact is that the healthy, normal immune system is up for the challenge," says Ponti, a spokeswoman for the Canadian Pediatric Society. "It's expansive. It takes these vaccines and runs with them, basically. It's challenged by them and it makes the child healthier."

Ponti calls immunization a child's best shot at staving off a lot of nasty diseases, everything from measles and mumps to whooping cough and chickenpox.

"It is a common misconception that these are just sort of benign childhood illnesses that we all have to go through," said the mother of two girls, aged two and three.

"You can die from all of these bugs. But death aside, having a life-long disability because of a preventable disease is to me tragic," she says, citing the potentially crippling effects of polio.

Chickenpox, traditionally considered a childhood rite of passage, can have serious complications, including a super-infection of the lesions that can lead to fatal blood poisoning, says Ponti.

Vaccines for chickenpox, pneumococcus and meningococcal meningitis have now been added to the immunization arsenal and will be covered by some provincial health plans starting next year.

The only shot Mathias-Geer and her husband Nik Geer might consider for their sons is tetanus, because the family has horses and the bacteria are carried in animal feces.

But as for chickenpox, Mathias-Geer thinks the dangers are being overstated because of the odd case of severe complications.

"They're taking these really rare examples and blowing them up to scare parents into getting this vaccine," she says. "A part of it I think is economic - not for the pharmaceutical companies - but for parents to not have to take time off work for the chickenpox."

A study published this week in Pediatrics seems, at least in part, to support her contention. Researchers say the vaccine has saved hundreds of millions of dollars each year in U.S. hospital costs since its 1995 introduction.

Still, needling fears about vaccine safety continue to fuel a debate about the human cost of immunization, especially after some parents linked the development of autism in their children to certain vaccines - measles-mumps-rubella (MMR) in particular - and a 1998 British study initially appeared to back them up.

That research turned out to be seriously flawed, says Dr. David Scheifele, director of the Vaccine Evaluation Centre at B.C.'s Children's Hospital in Vancouver, and subsequent research has shown no increased risk for autism due to the vaccine.

But the fallout from that study was a huge drop-off in MMR immunization, resulting in a dramatic rise in measles cases in the United Kingdom, Scheifele says.

"It's unfortunate to see a preventable disease reappear and make kids seriously ill based on flawed data," he says, noting that measles kills hundreds of thousands of children each year worldwide.

The B.C. centre has done almost 150 studies on various vaccines, including a decade-long one looking for any link between the pertussis, or whooping cough, vaccine and neurological problems like encephalitis, or swelling of the brain.

After screening tens of thousands of cases, the Canada-wide study found not one instance that could be pinned on the pertussis vaccine, says Scheifele. "Every single one of them on investigation had a much more plausible explanation.

"Canadian parents need to know that the vaccines being offered to their children are the safest we've ever been able to offer."

For Ponti, immunization is one of medicine's great success stories. But it's about more than limiting disease in today's children - it's also about protecting the next generation, she says. Exposure to rubella or chickenpox can damage the fetus if a woman gets pregnant and isn't fully immune to those diseases.

"You protect the children so that when they grow up, you protect their fetuses," she says. "And then you protect the adults (with boosters) . . . and they're not spreading it to the young infants. So it all comes around in a circle."

Mathias-Geer knows her children are beneficiaries of this "herd immunity" and that her decision to use good nutrition, a healthy lifestyle and homeopathic remedies instead of vaccines has generated anger.

"I get a lot of flak from parents saying, 'Well, we're taking the bullet for you.' But you know what? It's not my job to protect the world. And maybe that's a completely selfish view on this, but it's my job to protect my children, and everybody is within their rights to refuse vaccinations.

"Sometimes you just know in your gut that you're making the right decision."

Here is a list of vaccinations recommended by the Canadian Pediatric Society:

Diphtheria, tetanus, pertussis and polio (DTPP): Two, four and six months. Booster at 18 months and four to six years old. Tetanus-diphtheria adult booster recommended at 14 to 16 years old and every 10 years thereafter.

Hib (hemophilus influenza type b): Two, four and six months. Final shot at 18 months.

Mumps, measles, rubella (MMR): 12 months, then a second dose at 18 months or four to six years old

Hepatitis B: Infancy or at nine to 13 years old. In some jurisdictions, series of shots may be administered at a younger age.

Chickenpox: 12 months.

Pneumococcal: Two, four, six and 12 months. Protects against meningitis (brain infection), middle ear infection, pneumonia and infection of the blood or heart valves caused by the bacterium Streptococcus pneumoniae.

Meningococcal: Two and four months, then again at either six months or between 14 and 16 years old. Protects against meningococcal meningitis caused by the bacterium Neisseria meningitidis.