The Meditator reflects that he has often found himself to be mistaken with regard to matters that he formerly thought were certain, and resolves to sweep away all his pre-conceptions, rebuilding his knowledge from the ground up, and accepting as true only those claims which are absolutely certain. All he had previously thought he knew came to him through the senses. Through a process of methodological doubt, he withdraws completely from the senses. At any moment he could be dreaming, or his senses could be deceived either by God or by some evil demon, so he concludes that he cannot trust his senses about anything.
Ultimately, however, he realizes that he cannot doubt his own existence. In order to doubt or to think, there must be someone doing the doubting or thinking. Deceived as he may be about other things, he cannot help but conclude that he exists. Since his existence follows from the fact that he is thinking, he concludes that he knows at least that he is a thing that thinks. He further reasons that he comes to know this fact by means of his intellect, and that the mind is far better known to him than the body.
The Meditator's certainty as to his own existence comes through a clear and distinct perception. He wonders what else he might be able to know by means of this sure method. In order to be certain that his clear and distinct perceptions are indubitable, however, he first needs to assure himself that God exists and is not deceiving him. He reasons that the idea of God in his mind cannot be created by him since it is far more perfect than he is. Only a being as perfect as God could cause an idea so perfect. Thus, the Meditator concludes, God does exist. And because he is perfect, he would not deceive the Meditator about anything. Error arises not because the Meditator is deceived but because the will often passes judgment on matters that the limited intellect does not understand clearly and distinctly.
Secure in the knowledge that his clear and distinct perceptions are guaranteed by God, the Meditator investigates material things. He clearly and distinctly perceives that the primary attribute of body is extension and that the primary qualities of body are size, shape, breadth, etc. He also derives a second proof for the existence of God from the fact that, while bodies are essentially extended, God is essentially existent. A God that does not exist is as inconceivable as a body that is not extended.
Because the essence of body is extension and the essence of mind is thought, the Meditator concludes that the two are completely distinct. He decides also that while he can clearly and distinctly perceive the primary qualities of material things, he has only a confused and obscure perception of secondary qualities. This is because the senses are meant to help him get around in the world, not to lead him to the truth.