Descartes begins the Principles by attempting to throw all of our knowledge into doubt, so that we can determine whether there is anything certain among our beliefs. He then claims that even when everything is thrown into doubt, there is one proposition that remains indubitable: the proposition that he himself exists. Even to doubt his existence is a proof of his existence, because he could not doubt without existing. Descartes in now secure in the fact that there is at least one piece of knowledge so certain that it cannot be doubted. He asks whether there are more ideas like this, ideas that simply cannot be doubted so long as they are being entertained. He admits that there are other such ideas, such as the idea that two plus two equals four. He calls this class of ideas clear and distinct perceptions.

These ideas are extremely important because they cannot be doubted; because of their indubitableness they are the perfect building blocks for a systematic body of certain knowledge. Yet Descartes realizes that there is a problem with these ideas. Clear and distinct perceptions are only indubitable when they are being entertained. As soon as they fall out of awareness, doubt can creep back in. We can begin to wonder whether these ideas were caused by an evil demon, or were the product of a dream, or whether we even had them at all. In order to clear up this retroactive doubt, Descartes turns to God. Our idea of God, he claims, is of a being who is supremely and absolutely perfect. Perfection, he reasons, would not admit of willful deceit. God, as the creator of all the world, is certainly responsible for creating us and our faculty of reason. If he had created us such that what seems self-evident to the light of our reason is really false, then he would be deceitful, and thus imperfect. Clearly, then, God did not create us in this way. Instead, God must have created us so that what we perceive as clearly and distinctly true really is true. So long as we only rest our knowledge on clear and distinct perception, then, Descartes concludes that we can be sure of arriving at the truth. If we base our judgments on anything less than clear and distinct perception, on the other hand, we have no such guarantee, and will almost certainly fall into error.

Descartes gives two primary arguments for the existence of God. The first argument that Descartes gives of God's existence is commonly referred to as the "Ontological Argument". The Ontological Argument goes as follows: (1) Our idea of God is of a perfect being. (2) It is more perfect to exist than not to exist. (3) Therefore, God must exist.

The second argument that Descartes gives for this conclusion is far more complex. This argument rests on the distinction between two sorts of reality. Formal reality is the reality that anything has in virtue of existing. Formal reality comes in three grades: infinite, finite, and modes. God is the only existing thing with infinite formal reality. Substances all have finite formal reality. Finally, modes have modal formal reality. An idea, insofar as it is considered as an occurent piece of thought, has modal formal reality (since any particular thought is just a mode of mind).

Ideas, however, also have another kind of reality, unique to them. When considered in their relation to the objects they represent, ideas can be said to have objective reality. There are three grades of objective reality, precisely mirroring the three grades of formal reality. The amount of objective reality contained in an idea is determined solely on the basis of the amount of formal reality contained in the object represented by an idea. An idea of red has modal objective reality, because red has modal objective reality. An idea of a stone has finite objective reality, because stones have finite formal reality. Finally, the idea of God had infinite objective reality, because God has infinite formal reality.

It is the idea of God that is crucial to the causal argument. Descartes begins the argument by making the controversial claim that we all have an idea of God as an infinite being. (He believes that we cannot fail to have this idea because it is innate.) Because this idea is of an infinite being, it must have infinite objective reality. Next Descartes appeals to a logical principle: something cannot come from nothing. Reasoning from this principle he arrives at two other causal principles: (1) there must be as much formal reality in a cause as in an effect, and so, (2) there must be as much formal reality in a cause of an idea as there is objective reality in an idea. Since we have an idea with infinite objective reality (namely, the idea of God), Descartes is able to conclude that there is a being with infinite formal reality who caused this idea. In other words, God exists.

Descartes' argument that mind and body are two distinct substances, capable of existing apart, is based on two basic claims. The first is the claim that God can bring about the separation of anything that we can clearly and distinctly conceive of apart. Put another way, what this claim says is that if we can clearly and distinctly conceive of something existing on its own, then God can bring it about that this thing exists on its own. To deny this assertion, Descartes' thinks, is to call God a deceiver. The second claim the argument rests on is that both mind and body can be clearly and distinctly conceived without each other. The bulk of the argument is an attempt to prove the truth if the second claim.

For Descartes, to have a clear and distinct idea of a substance (rather than of a proposition) is to make a claim about the essence of the substance. It is to know the property that constitutes the very identity of the substance, the property that makes the substance the very thing that it is. What must be established in order to demonstrate that mind and body are distinct, then, is that there exist two different essences (intellectual activity and extension) and so two different corresponding substances (mind and body). Descartes uses an a priori thought experiment that consists in claims of conceivability, to establish his claims of essentiality. The first proposition (1), then, is that I can know that P is the essence of S, if and only if I can conceive of S attributing only P to it. Steps two and three use the thought experiment to establish that thought is the essence of mind. (2) I can conceive of mind attributing only thought to it. The proof of this is, in some sense, a corollary of the cogito. Now using step one he gets, (3) the essence of mind is thinking. Next in steps four and five, he must do for body what he has just done for mind. In other words, he must perform a thought experiment that isolates the essence of body. After doing this he arrives at (4) I can conceive of body attributing only extension to it. Again, drawing on step one, (5) the essence of body is extension.

He has proven that mind and body can both be clearly and distinctly perceived without each other. Now, using his claim that God can bring about the separation of anything that can be conceived of apart, he can conclude that mind and body are really distinct.