A MUM who has gone to court to fight her ex-husband's bid to have their children vaccinated says the procedure is akin to sterilisation or gender reassignment.

The mother, who cannot be identified, is fighting her former husband in the Family Court because she "vehemently opposes" his desire to vaccinate their two children.

She wants the court to declare immunisation a "special medical procedure", giving it the same legal status as sexual sterilisation and gender reassignment surgery.

To support her claims, the mother will call expert evidence from US doctors - and have her children undergo a battery of medical tests.

Since 2011, the Family Court has become increasingly involved in the vaccination debate.

In January of that year, it ordered a mother have her daughter, 5, immunised in line with the wishes of her former husband.

The girl's father, who has remarried and has another child, wanted the girl vaccinated against preventable diseases for her own wellbeing, and for the health of his other children.

In November last year, an eight-year-old Victorian girl continued to receive vaccinations against the objections of her mother.

The court heard the girl's father had been "secretly vaccinating" her during custody visits because he did not want to play "Russian roulette with her health".

MORE: What it's really like to grow up unvaccinated

The latest battle, between the parents of children dubbed "J" and "P" in court documents, is scheduled to commence on January 29 and last seven days.

Court documents do not give the ages, nor the genders, of J and P.

In a pre-trial application in April, the children's mother asked the court treat the father's proposal they be vaccinated as a "special medical procedure".

Under the Family Court Act, special medical procedures include sterilising intellectually-disabled girls, gender reassignment surgery, and lifesaving techniques opposed on religious grounds.

The mother also asked to call US-based doctors to support her claims, saying one specialist had quoted an appearance fee of $5000.

She said those overseas witnesses should be permitted to give evidence by telephone - the father objected, saying all testimony should be made in person.

In July the court ruled against the mother, saying she would have to call witnesses at her own expense and have the children undergo medical testing during her custody periods.

It permitted her doctors to test the children's blood, faecal and urine on the children, but not their food.

The mother subsequently lodged an appeal, saying the court lacked sufficient evidence to decide whether immunisation was a special medical procedure.

She claimed the decision demonstrated "bias and error", and showed the court had "failed in its duty of care".

The mother asked the trial be adjourned to provide her "sufficient time" to "research the relevant law" and further challenge the ruling.

In a judgment published on the court's website, Justice Ann Margaret Ainslie-Wallace dismissed the appeal and ordered the trial go ahead as scheduled.

"Whether or not (immunisation) is found to be a special medical procedure is a matter to be determined and argued before the trial judge," she says.

Originally published as Vaccination 'like sterilising' kids - mum