Board Thread:Questions and Answers/@comment-3444885-20141210002159/@comment-1672596-20141210010338

Alfrays wrote: Weedle McHairybug wrote:

Alfrays wrote: i don't think he even know that she gaved birth to his sons. As far as we know(from PW), he does not even belive that clones exist. Actually, I'm pretty sure Big Boss knew about the clones. After all, EVA DID specifically state that he left because of the Les Enfants Terribles project, meaning he definitely had to know about the clones (with EVA even stating to Solid Snake that he never wanted him in an apologetic tone.). i think that he left because he has discovered that they wanted to clone him, nothing more. Besides, even Miller talks like Snake knows nothing, like saying "i wonder how he wil respond to this" or something like this. Actually, just because Miller said "I wonder how he will respond to this" doesn't mean Big Boss didn't know. Don't forget, Miller didn't know about Cipher's plan to screw over MSF if Big Boss refused to rejoin by basically framing MSF with causing a nuclear attack on the East Coast.

And EVA made pretty clear that he knew about the clones, and even Big Boss basically confirmed as much in the ending of MGS4.