A western Sydney father has won the right to vaccinate his children following a drawn-out legal battle with their mother, who is strongly opposed to immunisation.

The Family Court rejected the mother's claims that the children, who will turn 14 and 12 this year, were at an increased risk of experiencing ''vaccine damage'' due in part to various allergies she believes they suffer from.

Sitting at Parramatta, Justice Garry Foster said the 42-year-old woman, given the pseudonym Ms Duke-Randall, had submitted hundreds of documents about the risks of vaccination, such as the link to autism, which has been thoroughly debunked by the medical profession.

Justice Foster said much of it was ''comments, submissions, irrelevancies'' and Ms Duke-Randall had become ''narrowly focused on it, perhaps to the point where the best interests of her children have been subsumed''.

The father, Mr Randall, 52, said during their marriage he agreed with Ms Duke-Randall's anti-vaccination view ''for the sake of peace in the household'' but, since their divorce in August 2011, he had come to realise his son and daughter were missing out on extracurricular activities because they were not immunised.