McCarthy, whose 11-year-old son has been diagnosed with autism, said that she's been "wrongly branded" as an anti-vaccine activist.
"I am not 'anti-vaccine,'" McCarthy wrote. "This is not a change in my stance nor is it a new position that I have recently adopted."
"My beautiful son, Evan, inspired this mother to question the 'one size fits all' philosophy of the recommended vaccine schedule," the 41-year-old continued. "What happened to critical thinking? What happened to asking questions because every child is different?"
McCarthy told Larry King in 2008 that she believed vaccinations could cause autism. She said at the time that she was not "anti-vaccine," but told King that she was treating her son's "vaccine injury."
"We're anti-toxin and we're anti-schedule. But the thing is, the way I treated Evan and the way a lot of the way these parents are treating their kids is not treating autism. We are treating vaccine injury and the kids are getting better," she said.
McCarthy reiterated that stance in her column over the weekend, saying that she still advocated for alternate vaccine schedules.
"For my child, I asked for a schedule that would allow one shot per visit instead of the multiple shots they were and still are giving infants."
"I believe in the importance of a vaccine program and I believe parents have the right to choose one poke per visit. I’ve never told anyone to not vaccinate," McCarthy added."I will continue to say what I have always said: One size does not fit all.” God help us all if gray is no longer an option."