The money from Gates and his wife, Melinda, is believed to be the largest charitable gift ever made, Fortune magazine said.
The donation includes $2.23 billion to the William H. Gates Foundation, named after and administered by Gates' father, and $1.11 billion to the Gates Learning Foundation, Gates spokeswoman Rose Berg-Fosnaugh said Friday.
The William H. Gates Foundation provides grants for health, population and education projects worldwide, and various causes in the Seattle area.
The Gates Learning Foundation, formerly the Gates Library Foundation, is dedicated to closing the gap between poor children and wealthier ones in Internet access and computer training.
Gates' Microsoft holdings are worth more than $82 billion.
In November, Gates donated $20 million to the Seattle Public Library. That was the biggest single gift ever made to a public library system, the spokeswoman said.