The charges include racketeering, corruption, fraud, tax evasion and money-laundering. It relates to the 1999 Arms Deal.
Thales has also pleaded not guilty to all the charges against it.
This marks the official start to Zuma’s corruption trial, although the matter is likely to be postponed, as Zuma has lodged a special plea – in which he argues that lead prosecutor Billy Downer must be removed.