The strip debuted in The Diamondback under editor Jayson Blair on December 3, 1996, paying McGruder $30 per strip — $17 more than other cartoonists. McGruder ended the strip's run in The Diamondback on March 18, 1997, two weeks after the strip was omitted due to a technical error and a Diamondback staffer printed the word "OOPS" in its place without an explanation. He pulled the strip after the paper refused to run an apology. (Upon the revelation in 2004 of news article fabrications by Blair, by then a reporter for The New York Times, McGruder's comic strip joined others in lampooning Blair.)
In Fall 2003, Boston, Massachusetts-based artist Jennifer Seng assumed art duties from McGruder. In an interview with The New Yorker, McGruder said, "If something had to give, it was going to be the art. I think I'm a better writer than artist." Carl Jones succeeded Seng as illustrator in late 2004. In the introduction to the collection Public Enemy #2, McGruder wrote, "I had hired an artist to help me on some of the art duties. People think I stopped drawing the strip, but that's never been the case. To this day there has never been a single Boondocks strip that I did not personally touch — I still obsess over the details of Huey, Riley, Caesar and Granddad. I still go over every panel. I still care what it looks like, and I always will."
On February 28, 2006, McGruder announced that his strip would go on a six-month hiatus, starting March 27, 2006, with new installments resuming in October. Repeats of earlier strips were offered by Universal Press Syndicate in the interim. The Boondocks was syndicated to over 300 clients at its peak, but more than half substituted different features rather than publish reruns during the hiatus.On September 25, 2006, Universal Press Syndicate president Lee Salem announced that the comic would not return, saying, "Although Aaron McGruder has made no statement about retiring or resuming The Boondocks for print newspapers ... newspapers should not count on it coming back in the foreseeable future." He added that Universal would welcome McGruder back if he chose to return. Greg Melvin, McGruder's editor at the syndicate, met with him in an unsuccessful attempt to talk the cartoonist into returning. McGruder cited his work on the Cartoon Network show among other projects as reasons for not then returning to the strip. After the strip was canceled, reruns continued to be carried by some newspapers through November 26, 2006.
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The strip depicts Huey Freeman and his younger brother Riley, two young children who have been moved out of Chicago by their grandfather to live with him in the predominantly white fictional suburb of Woodcrest (in Maryland, as seen from the area code stated in the March 16, 2000 strip). This relates to McGruder's childhood move from Chicago to a white, Maryland suburb. The title word "boondocks" alludes to the isolation from primarily African-American urban life that the characters feel, and permits McGruder some philosophical distance. Huey is a politically perceptive devotee of black radical ideas of the past few decades (as explained in the May 4, 1999, strip, Huey is in fact named after Black Panther Huey P. Newton) and is harshly critical of many aspects of modern black culture. For example, he is at least as hard on Vivica Fox and Cuba Gooding, Jr. at times as he is on the Bush administration. Riley, on the other hand, is enamored of gangsta rap culture and the "thug"/bling-bling lifestyle. Their grandfather is a firm disciplinarian who is offended by both their values and ideas.
Huey's best friend is Michael Caesar, a dreadlocked aspiring MC who agrees with many of Huey's criticisms but serves as a positive counterpoint to Huey's typically pessimistic attitude by taking a humorous approach to issues. He is also a budding comedian, although most of his humor consists of trying to play the dozens on Huey, which always falls flat. The Freemans' neighbors are NAACP member Thomas Dubois (a reference both to Uncle Tom and W. E. B. Du Bois) and his white wife Sara, who are both lawyers. Their young daughter Jazmine is very insecure about her ethnic identity and is often the subject of Huey's antipathy for being out of touch with her African ancestry. The Boondocks was very political and occasionally subject to great controversy, usually sparked by the comments and behavior of its main character, Huey. The comic strip has been withheld by newspapers several times. In this respect, it is similar to Doonesbury. In particular, the principal characters often discussed racial and American socio-economic class issues. Because of its controversy and serious subject matter, many newspaper publishers either relegated the strip to the op-ed section of the paper, pulled more potentially controversial strips from being published, didn't publish the strip at all, or canceled it altogether. These tactics have also been employed in other strips, such as Doonesbury.
- Huey Freeman - A cynical 10 to 14-year-old boy who appears angry most of the time, with strident political awareness, and who sees himself as a revolutionary. Named after Huey P. Newton, co-founder of the Black Panthers, he is disturbed by the ignorance in modern-day American society and media. An observant, intelligent child, he often finds himself playing the voice of reason. Huey is fond of some conspiracy theories, and completely distrusts all authorities.Thing is he never smiled in any of the comics!
- Riley Freeman - The opposite of his older brother, 8 to 12-year-old Riley praises the "thug life," and admires and emulates the rappers and thugs he sees on television. He has assigned himself the nickname "Esco", a reference to the rapper Nas christening himself "Nas Escobar" in the mid-1990s after infamous drug lord Pablo Escobar. He also formerly had the nickname "Yosemite Sam", but that appears to have faded away with time. Other aliases he's given himself have included "Osama Bin Laden" (chosen many months before 9/11) and Uday. Riley chose this last nickname on one of the extremely rare occasions he watched the news; he normally goes to great lengths to avoid the acquisition of knowledge. He once became upset after getting a C+ in school because he was afraid such "exemplary" grades would ruin his "street cred". Since asking for and not receiving rims for Christmas, Riley has been determined to sleigh-jack Santa Claus on Christmas Eve for the dual purpose of taking what he believes is owed to him and meting out punishment.
- Michael Caesar - Huey's classmate and best friend, who agrees with most of Huey's views of life. Unlike Huey, Caesar is more optimistic and cheerful, and usually jokes about whatever issue is at hand. It was Caesar's idea to find a boyfriend for Condoleezza Rice, reasoning that if she came to truly love somebody living on the planet she wouldn't be so "hell bent to destroy it." Caesar is originally from Brooklyn and needs little prompting to vocally represent his home town. He and Huey have co-founded the newsletter the "Free Huey World Report" and the annual "Most Embarrassing Black People Awards."
- Robert Jebediah "Granddad" Freeman - Huey and Riley's retired grandfather, a pragmatist and disciplinarian who usually sees through the shenanigans of his grandsons. Robert is known to panic at news reports, and values his own peace and comfort over the needs of others while still looking out for the children's welfare.
- Thomas and Sara Dubois - An interracial couple in the neighborhood. They both work as lawyers. Tom is often seen talking (sometimes arguing) with Huey about current politics, while Huey tends to deride Tom for being a conformist yuppie, sometimes going so far as to sarcastically suggest that he's not really black. For a while Tom was kicked out of the house by Sara after he called her a "two-timing political floozy" when she voted for Ralph Nader instead of Al Gore. Four years later, Tom kidnapped Nader in hopes of preventing him from taking votes away from John Kerry and costing the Democrats the 2004 Presidential Election. Huey eventually persuaded him to release Nader.
- Jazmine Dubois - Thomas and Sara's biracial, 10-year-old daughter, who seems to like Huey, despite his general coldness toward her. She is notable for her insecurity over her biracial status. Jazmine is often portrayed as naïve, and is optimistic in contrast to Huey's pessimism. Early in the strip she was deliberately ambiguously colored so as to cloud the issue of whether she was white or black. It even prompted her to be directly asked by her teacher. She disappeared for roughly two years, and it was revealed she had been so frightened of terrorists that she would not leave her house. She tried to turn herself in to the FBI three times, because she thought she was helping the terrorists by being scared (having heard statements to the effect that "If you live in fear, the terrorists win"). She eventually came out because of a "Credible threat against her teddy bear." Jazmine is insecure about her curly and voluminous hair, wishing it looked straighter, like her mother's hair. Huey's suggestion to Tom that he and Sara try "emphasizing the natural beauty of her African features" rather than trying to help her change her appearance fell on deaf ears. On one occasion when Jazmine was complaining about her "big and poofy" hair, Huey interrupted her to ask what she thought of clouds. She thought clouds were pretty, but completely missed the point Huey was trying to make.
- Cindy McPhearson - A Caucasian girl in Huey's class who appears to be utterly clueless about racial issues. She shows a fondness and curiosity for rap music, particularly Snoop Dogg.
- Hiro Otomo - One of Huey's friends, a young Japanese-American DJ. Hiro only appeared in the original Diamondback version of the strip. He is named after mangaka Katsuhiro Otomo.
- The school principal - An out-of-touch white man who prepared for the arrival of Huey and Riley by renting several blaxploitation films, mistakenly thinking of them as representative of black culture. He somehow has access to FBI files of Huey.
- John Petto - Huey and Caesar's white teacher, who is as clueless about how to handle them as the principal is. Old-fashioned and not used to dealing with blacks, he is intimidated by Huey's intellect and has struggled trying to debate with Huey during class.
The content of McGruder's comic strip often came under fire for being politically left-wing and occasionally risque, leading to its being published in the op-ed section of many newspapers. For example, a strip making fun of BET's rap videos, some of which rely on the sexually suggestive gyrations of female dancers, and a strip mocking Whitney Houston's drug problems and emphasizing her buttocks, were pulled out of circulation. The Boondocks garnered significant attention after the September 11, 2001 attacks with a series of strips in which Huey calls a government tipline to report Ronald Reagan for funding terrorism. Soon after, he "censored" several strips by featuring a talking patriotic yellow ribbon and a flag (named Ribbon and Flagee, respectively) instead of the usual cast.
Several strips have been briefly pulled from prominent publications. For example, the "Condi Needs a Man" strip, in which Huey and his friend Caesar create a personal ad for U.S. Secretary of State Condoleezza Rice, portraying her as a "female Darth Vader type that seeks loving mate to torture", resulted in The Washington Post withholding a week's worth of strips, the longest such suspension ever by the paper. However, the paper's ombudsman, Michael Getler, later sided with McGruder.  The Post also declined to run "Can a Nigga Get a Job?", which had black contestants compete on a reality TV show to work for Russell Simmons, only to find that all the contestants were rude and lazy. This unflattering portrayal drew the ire of many in the African American community.
McGruder wrote a strip where Huey and Caesar discuss the "Most Embarrassing Black Person of the Year Awards", which they dub the "Elder" after Neocon Black commentator Larry Elder. In response, Elder published an opinion piece in which he created the "McGruder Awards", naming liberal commentators, and including six quotes from McGruder.