This post must be a rapid summary of punctuation rules and practices; otherwise, we will both be here all day. If you need the full tour of all punctuation principles, use a “style manual” for reference. Newspapers, magazines and publishing houses have created such style manuals as the rules and regulations for anyone who writes copy for them. The most famous is The New York Times Manual of Style and Usage. The Associated Press (AP) Stylebook is also well-known and highly regarded. The Government Printing Office also prints one, blandly called The Government Printing Office Style Manual (usually abbreviated to “GPO”). Law journals mostly use the Uniform System of Citation published decades ago by the Harvard Law Review. While it addresses itself mainly to citation forms, it also touches on other aspects of correct usage. These authorities do not always agree with each other, but they do unanimously sanction most of the basic principles.
The Internet is an excellent source of guidance on punctuation; however, exercise caution: not everyone who uploads his opinion is uniformly correct (including yours truly, I suppose). A discerning researcher will note some inconsistencies among the various resources available. As in the case of dictionaries, some sites are more conservative, and advocate only orthodox usage; others are more liberal and will acknowledge and accept many usages even though they are mistakes, just because they are widespread. The more conservative ones should be looked to as normative: authorities; the more liberal ones should be deemed merely descriptive: catalogues of usage.
A free, online style manual that takes a traditional approach to Standard American English is the one produced by the National Geographic Society.
The Basic Concept

The most basic principle, the bedrock fundamental, can be illustrated by the following anecdote: Once I was helping Manolo to study for his GED exam. Manolo was from Mexico, and his exam was to be administered in Spanish. Though fluent in his mother tongue, he needed considerable help with writing. His word choices were correct, more or less, but his spelling was, well, non-standard. Worse yet, his punctuation (including accent marks) seemed random. When asked, he confirmed that indeed it was random! He believed that accents and punctuation marks should be spread around one’s writing as decorations, in the same way that one scatters seeds in a garden plot. This is similar to the “sounds right” approach to grammar in general: It is lawless, unreliable and tragically ignorant. Fortunately, ignorance is curable, as proved true in Manolo’s case. (On the other hand, stupidity, sadly, is not.)
In short: Every punctuation mark exists for one or more reasons. Learn the reasons, and follow the rules. Do not fall into the fallacies of the “sounds good” method or the randomizing approach.
Here is a runner’s dash through the rules:
Periods
Use them for ending sentences. Use them after most abbreviations. An elipsis (…) is not a series of three periods. It is an elipsis and has its own function, which is to indicate omission.
Question Marks
Use them after direct questions; do not use them after indirect questions. Compare: “How old are you?” and “He asked me how old I was.”
The question mark goes inside the closing quotation mark if it is part of the quotation; otherwise, it is outside the closing quotation mark: He asked, “How old are you?” versus Did you hear him say, “I am am 21 years old”?
Exclamation Points
Use them after exclamations (duh!) and all but mild interjections: “I’m lost!” “Wow!” “Sorry, I didn’t know.”
Commas

Commas are the most common form of punctuation (pun intended), and the most abused. This is a partial list, as commas come up in so many contexts. For a complete rundown, consult a manual of style. Use Commas:
- To separate words in a series “(Porthos, Dartagnan, Aramis and Athos”). Note: the comma after the next to last item is usually omitted in modern texts, but it is not wrong to insert it, and it may occasionally avoid confusion (as in the following Sky News headlines summary from December 10, 2013: “Top Stories: World leaders at Mandela tribute, Obama-Castro handshake and Same-sex marriage date set”). It is called “the Oxford comma.”
- To separate phrases in apposition (“My uncle, the judge, was always sober.”)
- To separate introductory clauses. (“Because you asked politely, I shall do it.”)
- To separate many, but not all, subordinating conjunctions from the rest of the dependent clause in a complex sentence. (“It snowed; however, we went anyway.” But: “I shall do it because you asked politely.”)
- To separate coordinating conjunctions from the preceding independent clause in a compound sentence. (“She likes country, and I like rock ‘n’ roll.”)
- In a variety of specific contexts:
- After the salutation in an informal (friendly) letter (“Dear John,”)
- To separate repeated words (“I really, really want a puppy!”)
- To introduce a quotation (W.C. Fields said, “Never give a sucker an even break.”)
- Before of after directing a statement to a person or thing (“Houston, we have a problem”; “No, Perkins.”)
- After mild interjections (“My goodness, that was a long speech.”)
Semicolons
Use them to separate:
- Independent clauses from the subordinating conjunction in a complex sentence (but not in every case). (“It snowed; however, we went anyway.” But not “I like you because you never complain.”)
- Independent clauses in a compound sentence, if there is no coordinating conjunction. (“It was the best of times; it was the worst of times.”)
- Items in a series, if the items are long phrases or clauses. (“I plan to get up early; put all of last night’s dishes in the dishwasher; go shopping; make dinner for everybody; and then spend some time on my own projects.”)
- Items in a series, if one of the items is internally punctuated by commas. (“I will clean the pasture spring; rake the leaves away; and, if there’s time, wait to watch the water clear.”)
Colons

Use colons to separate the first part of a sentence from the rest, if it is an introduction to the next part, and the next part is really an explanation or more detail. (Here is my idea: we should go eat.) Colons are also used to separate hours and minutes when writing time (10:47 p.m.), and at the end of salutations in business letters (Dear Sir or Madam:).
Quotation Marks

- Enclose direct quotes in quotation marks, but not indirect quotes. (He said, “You should go”; He said that I should go.)
- Quotation marks are also used to signal words employed in a non-standard or ironic way. This usage gave rise to “air quotes” in spoken conversation. (W.C. fields kept a jug of “pineapple juice” on the movie set.)
- When referring to a word or number as such (rather than to its meaning), you should italicize it and put it in quotation marks. (Is there an “a” in “perimeter”?)
- A period or a comma should go inside the closing quotation mark, even if it is not part of the quote. Semicolons and colons reside outside the closing quotation mark, unless part of the quotation. This rule for semicolons and colons also applies to question marks and exclamation points. (The Wikipedia Style Manual applies the semicolon and colon rule to periods and commas as well, but that puts it in a small minority. Virtually all style manuals for journalists and authors apply the rule for periods and commas stated here.)
Apostrophes

Apostrophes indicate:
- Omissions, as in a contraction. (“Do not” becomes “Don’t.”)
- Possession. (“John’s gospel”; “It is anyone’s game.”)
- Plurals in the limited context of letters of the alphabet. (There are four s’s in “possess.”) Please don’t use apostrophes for normal pluralization!
- Quotations internal to a quotation. (Actually, these are “single quotation marks,” not apostrophes.) (W.C. Fields famously said, “What rascal has been putting pineapple juice in my ‘pineapple juice!’”)
Capitalization

- Of course, you know to use initial capitals at the beginning of a sentence (but not at the beginning of a clause internal to the sentence). (This clause starts with an initial capital; this clause does not.)
- You also know that proper nouns (like “Texas”) and their derivatives (usually adjectives, like “Texan”) are capitalized. This includes the names of persons (including their titles, like “Monseigneur” or their roles, when used as a name or title, like “Mommy”), countries (“Rwanda”), geologic eras (“Paleozoic”), historical periods and events (“the Middle Ages,” “World War I”), days (“Wednesday”), months (“October”), holidays (“Labor Day”), but not seasons (“spring”) or centuries (“the seventeenth century”). “God” and all pronouns referring to Him are capitalized. Most authorities capitalize abbreviations that are titles (“Mr.” or “Prof.”), but otherwise, not (“a.m.” and “etc.”).
- The pronoun “I” is capitalized; “me,” “my” and “mine” are not.
- The major words in titles also are capitalized. There are a few nuances to this: Verbs, even small ones like “is,” should be considered major words in a title (“Reading Is Fundamental”), while articles and prepositions are not (“Gone with the Wind”). The initial word in a title must be capitalized, even if it is not otherwise a “major” word (“On the Waterfront”).
A Note About Accent Marks
Diacritical marks (loosely called “accent marks”) are as much part of spelling as are the letters in a word. Because English does not use many diacritical marks, it is easy to be blasé about them. Spell checkers do not like them. BUT: they are required if you wish to be technically correct. For example, the famous English playwright, Noël Coward, who was born on December 16, was named (apparently) after Christmas en français: (Noël). Almost everyone writes his name (and pronounces it) as if the two little dots — the diaeresis — were not there: “Noel Coward.” “Naïve” is another import word that seems to be gradually losing its diaeresis in English. We still seem to be hanging on to the accents in “canapé” and “touché,” however. The word “fête” (meaning party or festival) needs its circumflex accent, too. “Agape” means “wide open” in English. “Agapé” means love of men and mankind as brothers.
You may get through life with only the most sporadic need for accent marks in English. The greater risk is in thinking that by adding one where it does not belong, you will seem more sophisticated. For those who know better, it’s really rather pathetic. There is a hotel in Colorado Springs called “Hotel Eleganté.” The accent mark is a misfit in English; it is also an error in French, Spanish, and in every other romance language. Even the perpetrators of this barbarism fail to pronounce the accent, putting the emphasis instead on the next-to-last syllable (as it should be). So I guess they intend it to be a “non-accent” mark. Try not to commit this kind of ignorant mistake; it’s bush-league and completely avoidable.
A small correction from a fellow Yalie: ‘however’ isn’t a subordinating conjunction, but a conjunctive adverb. Thus there’s no inconsistency between putting commas around ‘however’ but no commas around ‘because’, since they’re quite different parts of speech (‘because’ is, as you say, a subordinating conjunction).