To cite the Summa theologiae [ST], state the part (I, I-II, II-II, or III), the question number (q. 75), the article number (a. 1), the section of the article—either the objections (arg. 1); the "on the contrary" section (sc.); the body of the article, which starts "I respond that..." or "I answer that..." (co.); or the replies to objections (ad1). Here are some examples:

ST I, q. 75, a. 1, arg1

ST II-II, q. 2, a. 1, co.

ST I-II, q. 1, a. 1, ad2.

To cite Aquinas's short treatises, On Being and Essence (De ente et essentia) or On the Principles of Nature (De principiis naturae), just give the title of the book followed by the chapter number, like this: c. 2, for chapter 2. If your edition includes paragraph numbers, you can cite the paragraph numbers too, like this §3 (for paragraph 3). If you want to cite the page numbers (or if your instructor tells you to do so), you can do so like this: pg. 254. Here are some examples:

On Being and Essence, ch. 1, §2, pg. 3.

Or without paragraph and page numbers.

On Being and Essence, ch. 1.

Citing books divided into chapters (e.g., On Being and Essence; Summa contra Gentiles)

Some of Aquinas's books, such as On Being and Essence (De ente et essentia), On the Principles of Nature (De principiis naturae), and On Separate Substances (De substantiis separatis) are organized by chapter. These are the easiest works to cite since you can just cite them by chapter. 

Here's an example. Suppose I want to cite where Aquinas says that the essence of a composite substance is both matter and form. The way I would do this is by writing the following either in a footnote or in parentheses:

Aquinas, On Being and Essence, c. 2.

Suppose, however, you wanted to cite the place where Aquinas says that a small mistake in the beginning leads to great mistakes later on. Well, that is not in any of the chapters of On Being and Essence, but in the prologue. So, you can cite it as follows:

Aquinas, On Being and Essence, pr.

Or, if you don't like abbreviations, as follows:

Aquinas, On Being and Essence, prologue.

It is that easy! It is only slightly more complicated to cite Aquinas's great apologetic work, the Summa contra Gentiles, and his unfinished catechetical treatise, Compendium theologiae. These works are divided first into "books" and then into chapters. Let's just look at Summa contra Gentiles. This is divided into four "books." These are very broad topics under which a series of chapters are included. Book 1 is about God's existence and nature. Book 2 is about creation. Book 3 (two parts in the Notre Dame English translation) is about divine providence—that is, God's mode of governing creation. (This covers topics like good and evil.) Book 4 is about the Trinity, the Incarnation, the sacraments, and the afterlife. If you want to cite the Summa contra Gentiles, you just indicate which of the four books you are citing and, then, which chapter from that book. Here's an example:

Aquinas, Summa contra Gentiles I, c. 13.

Here's another example, this time citing Book 3 instead of Book 1.

Aquinas, Summa contra Gentiles III, c. 25.

Citating commentaries divided by lessons / lectures (lectiones) (e.g., Commentaries on Aristotle)

Much of medieval philosophy is found in commentaries on authoritative books—on sacred scriptures, on Aristotle's works, and so on. In these commentaries, medieval authors aimed not only to explain the sense of the text—that is, to make it easier or more intelligible for those who read it—but also to explore the philosophical implications of the principles and ideas laid out by the ancient author whose work they commented upon.

Most of Aquinas's commentaries on Aristotle are divided into multipled "books" (think of these as parts of a single book) and then lectures or lessons (lectiones) (which are basically the same thing as chapters). Let's take Aquinas's commentary on Aristotle's Metaphysics as an example. If we want to cite Aquinas's lecture on the meaning of "being," we would do so as follows:

Aquinas, In V Metaphysics, lec. 9.

Here, the word "In" indicates that we are citing what Aquinas says about (or "in") Aristotle's work, the Metaphysics. The Roman numeral "V" indicates that we are looking at Book 5 of Aristotle's work. The abbreviation "Lec. 9" indicates that we are citing lesson 9 of Book 5. 

In some editions of Aquinas's commentaries, there are also running paragraph numbers throughout the lectures. It is good to cite these as well. So, for example, if you want to cite the place where Aquinas distinguishes between multitude (discrete quantity) and magnitude (continuous quantity), you would say:

Aquinas, In V Metaphysics, lec. 15, 978. 

That's because he discusses this in the 978th paragraph, which is found in lesson 15 of Book 5 of Aquinas's commentary on Aristotle's Metaphysics.

Citating books in the disputed questions format (e.g., Summa theologiae; Disputed Questions on Truth)

Introduction

In medieval universities, many classes would be held in the disputed questions format. This is basically a heavily structured debate. One set of students would give arguments for opinion p. Another set of students would give arguments for opinion not-p. Then, the instructor would come in and settle the debate by both answering the question at hand and then responding to the arguments from both sides with which he disagreed.

Citing the Summa theologiae

In Aquinas's famous theological textbook, the Summa theologiae (abbreviated "ST"), this format is replicated in writing, but in a heavily simplified way. In general, in each article, Aquinas first lays down a topic for debate. This is the title of the article (abbreviated as "tit."). For instance, in ST I, q. 2, a. 3, the title can be translated either as "Whether God exists?" (utrum deus sit). 

Aquinas then presents several objections. These represent arguments from students against the view that God exists. These objections (abbreviated as "arg." or "obj." depending on your preference) do not represent Aquinas's view, but are what we may call the "devil's advocate" position. 

Next, Aquinas presents one or two (rarely more) short arguments—usually from authority—for the opposition position to the one found in the objections. This section is called the "sed contra," which literally means, "But on the contrary..." The abbreviation for citing this section is "sc." for "sed contra."

After giving a short argument in the sed contra, Aquinas gives his magisterial answer to the topic at hand. So, for instance, in ST I, q. 2, a. 3, he gives five proofs that God exists. The section where his magisterial answer to the topic is found is called the "corpus" or the "respondeo" (abbreviation "co." or "resp.") since it usually begins with the words, "I answer that" or "I respond that" (respondeo).

Finally, Aquinas responds to each of the objections raised at the start of the article. Since the Latin word for "to" as in "Aquinas is responding to the objection" is the word "ad," we cite these responses as "ad" followed by the number of the response.

Now, the Summa theologiae is divided not only into articles (i.e., mini-debates, like we have just described), but also into "books" (very broad topics), and "questions" (narrower topics). Specifically, it is divided into three books. Book 1 (abbreviated with the Roman numeral "I") has to do with God and creation in general. Book 2 has to do with man's road to God (i.e., ethics or morality). This book is itself subdivided into two parts. Part 1 of Book 2 (abbreviated "I-II") is Aquinas's more general moral theology. Part 2 of Book 2 (abbreviated "II-II") is his more specific or detailed moral theology. Part 3 (abbreviated "III"), which is unfinished, contains Aquinas's discussion of the Incarnation and the sacraments. After Aquinas's death, his students finished Part 3. This added section of Part 3 is called the Supplement to the Summa or just the Supplement. 

Each of these books is divided into "questions" (abbreviated "q."), which are not actually questions, but rather subtopics. So, for instance, ST I, q. 79 is about the intellectual powers of the soul. It is not really a question, but is actually divided into thirteen "articles" (abbreviated "a."), which are the real questions. This can be a little confusing, but just remember that "questions" are really subtopics whereas "articles" are really questions.

Okay, let's look at an example. Suppose you want to cite Aquinas's argument for the immortality of the soul. Well, this is found in the corpus of a. 6 of q. 75 of the First Part of the Summa. So, you would cite it as follows:

Aquinas, ST I, q. 75, a. 6, co.

Let's say you wanted to cite the third objection from this same article. (Again, remember that Aquinas does not agree with the objections! Still you may want to cite them to explain his reply.) You would do so as follows:

Aquinas, ST I, q. 75, a. 6, arg3.

If, then, you want to cite his reply to the third objection, you can do so as follows:

Aquinas, ST I, q. 75, a. 6, ad3.

Suppose now, you want to cite the place where Aquinas proves that happiness does not consist in wealth. Well, this is in the corpus of article 1 of question 2 of the First Part of the Second Part of the Summa. Thus, you cite it as follows:

Aquinas, ST I-II, q. 2, a. 1, co.

Citing other disputed questions

This basic format will help you, with slight variations, cite many of Aquinas's works, including his Commentary on Boethius's De trinitate, his Commentary on Peter Lombard's Sentences, Disputed Questions on Truth, Disputed Questions on the Power of God, Disputed Questions on Evil, and so on.

For example, the commentary on Boethius's De trinitate is divided into questions and articles, but lacks book divisions. So, you can cite it like this:

Aquinas, In De trinitate, q. 5, a. 3, ad3.

The standard textbook for theology students in the Middle Ages was Peter Lombard's Sentences, which was called "the Sentences" because it was primarily a collection of quotations or judgments (sententiae) from the Church Fathers on various theological topics. Lombard tried to draw out unsettled questions or debates among the Church Fathers to stimulate further reflection. To receive a Master's degree (equivalent to a modern doctorate), students in the Middle Ages had to lecture on the entirety of Lombard's Sentences. Aquinas's commentary on this work is the fruit of those lectures. You cite the Sentences commentary in much the same way you cite the Summa except that it is divided into four books and the books are divided first into "distinctions" (subtopics, abbreviated "d.") and then into "questions" (sub-subtopics, abbreviated "q.") and finally into "articles" (questions, abbreviated "a."). Here's an example:

Aquinas, In I Sent., d. 8, q. 4, a. 1, ad2.

Variations in style

The exact abbreviations I have used are not totally standardized. So, for instance, you may see the Summa theologiae parts abbreviated as "Ia" (for Latin prima pars), "Ia-IIae" (for prima secundae pars), "IIa-IIae" (for secunda secundae pars), "IIIa" (for tertia pars) instead of "I," "I-II," "II-II," and "III," as I have done. You may even see these abbreviated as "1," "1-2," "2-2," and "3," or some other slight variation. Likewise, you may see the Summa theologiae itself abbreviated as "STh" or something similar. Sometimes you'll even see the name of the Summa theologiae spelled differently as Summa theologica. This is the same thing, just a more modern Latin spelling. (For further reading on some of these variations, see Douglas Beaumont's article on the matter.)

When you cite works outside the Summa theologiae, the nice subdivisions I described above sometimes break down. If you are having trouble figuring out how to cite a particular section—say an expositio or a prologue—a good rule of thumb is to look at how they cite it on Corpus Thomisticum, where every paragraph is prefaced with a citation.

1. First click Opera omnia S. Thomae on the Corpus Thomisticum homepage.

2. Find the work and section of that work you want to cite.

3. Look for the paragraph you want to cite and follow the citation given above that paragraph.

Critical editions are editions of works, which contain a "critical apparatus." The critical apparatus is a series of notes (usually at the bottom of the page), which indicates all the variations between the various manuscripts from which the type-written edition was made. Ideally, a critical edition will be based on all the surviving, available manuscripts of a work or all the more principal ones, and it will indicate at the bottom all the differences between the various manuscripts. 

For the critical editions of Aquinas's works, see the Books by Aquinas tab. The main series of critical editions of Aquinas's works is the Leonine edition. To cite a critical edition, just follow the instructions above for basic citations and then add in parentheses to the end of your citation a note indicating which edition was used, followed by the page and line numbers to which you are referring in that edition. Styles for doing this vary considerably, but these examples should get the point across. 

Aquinas, In I APo., l.33: “Est ergo differencia in tribus modis predictis quia, cum predicatur accidens de subiecto, non predicatur per aliquod aliud subiectum; cum autem predicatur subiectum de accidente uel accidens de accidente, fit predicatio ratione eius quod subicitur termino posito in subiecto, de quo quidem predicatur aliud accidens accidentaliter, ipsa uero species subiecti essencialiter” (Leonine ed., vol. 1*/2, p. 121, lns. 113–20).

Aquinas, In I APo., l.33: “Est ergo differencia in tribus modis predictis quia, cum predicatur accidens de subiecto, non predicatur per aliquod aliud subiectum; cum autem predicatur subiectum de accidente uel accidens de accidente, fit predicatio ratione eius quod subicitur termino posito in subiecto, de quo quidem predicatur aliud accidens accidentaliter, ipsa uero species subiecti essencialiter” (Leon. ed., 1*/2.121:113–20).

Aquinas, In I APo., l.33 (Leon. ed., 1*/2.121:113–20).

All of these citations are meant to cite Aquinas's commentary on the Posterior Analytics, lecture 33. The passage in question is found in the second part of the second edition of volume one of the Leonine edition of Aquinas's complete works (1*=second edition of volume one; 1*/2=second part of second edition of volume one). It is found on page 121, in lines 113–20.