Given that God is not a deceiver, Descartes next asks, how is it possible that human beings come to make mistakes? The answer, as Descartes shows in principles I.32 through I.44, is that error results only when we form judgments about perceptions that are not clear and distinct. So long as we only assent to clear and distinct perceptions, we will never fall into error.

The fact that we err, then, cannot be seen as an imperfection in the way that God made us. God made us as perfectly as was possible. He gave us, first of all, an infinite will so that we could act voluntarily and thus be considered responsible for our own actions. He also gave us an understanding, capable of showing us clear and distinct perceptions. Our understanding, though, unlike our will, is not infinite. We only understand what we have already reasoned correctly about.

Descartes' claim that God gave us an infinite will leads him into a brief discussion of the problem of free will, in principles I.40 and I.41. Since we know that God is omnipotent and the author of all that occurs, we know that everything that happens is preordained by God. How, then, he asks, can we reconcile this with the idea that we are free to act however we choose? Descartes' answer is surprisingly disappointing. We can reconcile it, he says, by realizing that we do not understand everything about God. In other words, he has no idea how to reconcile it, but that does not mean that it is irreconcilable.

In principle I.40 Descartes moves back from God to clear and distinct perceptions themselves. First he tells us precisely what he means by the term "clear and distinct perception." By calling a perception "clear" he means to say that we fully grasp what is contained in it. To perceive an idea clearly is much like seeing an object in good light. A perception is "distinct," on the other hand, when we also fully grasp what it does not include. A perception can be clear without being distinct, but not vice versa. Pain, to use Descartes' own example, is very clear. It is not, however, always distinct, because people often think that pain is some actual thing existing in the part of the body that feels painful. They do not realize that pain is only a sensation. So though they clearly feel the pain, they do not distinctly perceive what is and is not included in this sensation.

Descartes now begins the main project of the text. He has established his method (i.e. find clear and distinct perceptions, use these to logically derive further clear and distinct perceptions, and so on), and now he is going to implement it. In I.47 he begins an inventory of all of our ideas and asking which of them are clear and distinct. In other words, he is trying to find some more of these all- important ideas so that he can use them to build up his system of certain knowledge. (Remember that up until this point, all he knew for certain was his own existence, God's existence and nature, and a few truths of mathematics).

The first step to this inventory is the division of all ideas into three categories. All of our ideas, Descartes tells us in I.47, belong to one of three types: either they are ideas of things (i.e. substances), the ideas of affections of things (i.e. properties or qualities of substances), or the ideas of eternal truths.