With end-to-end encryption, messages are scrambled as they leave the senders device and can only be decrypted by the recipients device.
It renders messages unreadable if they are intercepted, for example by criminals or law enforcement.
Whatsapp, which has a billion users worldwide, said file transfers and voice calls would be encrypted too.
Encryption was thrown under the spotlight after the FBI asked Apple to help it access data on an iPhone used by California gunman Syed Farook.
Users with the latest version of the app were notified about the change when sending messages on Tuesday. The setting is enabled by default.
Other messaging apps with end-to-end encryption include Telegram, which is known to be used by the so-called Islamic State to share information.
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