Mr Zuckerberg made the announcement in a letter to Max on his Facebook page.
He said they were donating their fortune to the Chan Zuckerberg Initiative to make the world a better place for Max to grow up in.
The donation amou nts to $45bn (£30bn) at Facebook’s current value.
However the shares will not be donated to charity immediately, but over the course of the couple’s lives.
Were Mr Zuckerberg to give away 99% of his shares immediately, he would still possess hundreds of millions of dollars. Ms Chan’s worth has not been documented.
Max was born last week, although her birth was only made public on Tuesday.
In his letter Mr Zuckerberg said the aim of the Chan Zuckerberg Initiative is “to advance human potential and promote equality for all children in the next generation”.
Its initial areas of focus will be personalised learning, curing disease, connecting people and building strong communities.
“Your mother and I don’t yet have the words to describe the hope you give us for the future,” Mr Zuckerberg said at the start of his letter to Max.
“You’ve already given us a reason to reflect on the world we hope you live in,” it added.
SOURCE – BBC NEWS