Paying for It (2011) drew controversy as a polemic in support of decriminalizing prostitution, a theme he explored further with Mary Wept Over the Feet of Jesus (2016), a book of adaptations of stories from the Bible that Brown believes promote pro-prostitution attitudes among early Christians.

At around twenty, Brown's interests moved away from superhero and monster comic books towards the work of Robert Crumb and other underground cartoonists, Heavy Metal magazine, and Will Eisner's graphic novel A Contract with God (1978).

He became friends with film archivist Reg Hartt, and the two unsuccessfully planned to put out a comics anthology called Beans and Wieners as a showcase for local Toronto talent.

[3] While he found it difficult at first, Brown managed to get the title into independent bookstores, the emerging comic shops, and other countercultural retailers, and also sold it through the growing North American zine network.

[13] Brown began to weave together some of the earlier unrelated strips[14] into an ongoing surreal black comedy called Ed the Happy Clown.

What appeared a natural target of satire for the author of Ed was instead a continuing attempt of Brown's to find what he really believed, having been raised a Christian Baptist.

The offensive content of Ed caused it to be dropped by one printer,[17][18] and is suspected to be behind Diamond Comic Distributors' decision to stop distributing Yummy Fur starting with issue #9.

At this point, Brown had grown to lose interest in the Ed story[21] as he gravitated toward the autobiographical approach of Pekar, Joe Matt, and Julie Doucet,[22] and the simpler artwork of Seth.

[25] With "Showing 'Helder'" Brown breaks from his earlier syle by giving the panels no borders and arranging them organically on the page—a style that was to characterize his work of this period.

The revealing, confessional story tells of the teenage Brown's feelings of guilt over his obsessive masturbating over the Playmates of Playboy magazine, and the difficulties he had relating to women even into adulthood.

Its lead character, Kupifam, was an infant who was surrounded by an encoded[a] gibberish-like language, which she comes to understand in bits and pieces.

Brown came to decide that he no longer wanted to have exclusive relations with women, but also realized he lacked the social skills to pick up girls for casual sex.

He lost interest in Underwater, and had been reading about Métis resistance leader Louis Riel, and decided he wanted to do a biography on him.

[34] Drawn & Quarterly put out the ten issues of Louis Riel from 1999 until 2003, and with help from a CAD$16,000[10] grant from the Canadian Council for the Arts,[35] the finished annotated collection appeared in 2003, to much acclaim and healthy sales.

In the early 2000s, Brown moved out from the place he shared with Lee and got himself a condominium, where he lived by himself, and was free to bring prostitutes home.

[41] In 2007 Brown provided six weeks worth of strips to Toronto's NOW magazine as part of the "Live With Culture" ad campaign.

The strip features a male zombie and a living human girl participating in various cultural activities, culminating in the two going to a movie theatre to watch Bruce McDonald's yet-unmade Yummy Fur adaptation.

[44][45] It was a polemic promoting the decriminalization of prostitution, and attracted praise for its artistry and bare-all honesty,[46] and criticism for its subject matter and Brown's perceived naïveté as he brushes aside concerns about human trafficking[47] and dismisses drug addiction as a myth.

Brown describes himself as a Christian who is "not at all concerned with imposing 'moral' values or religious laws on others" and believes that Biblical figures such as Abel and Job "find favour with God because they oppose his will or challenge him in some way".

After attending a few meetings of the Libertarian Party of Canada, he was asked to run for Parliament, and collected the 100 signatures necessary to appear on the ballot.

[59] A longtime friend of fellow cartoonists Joe Matt and Seth, Brown has been regularly featured in their autobiographical comics over the years, and collaborated with them on various projects.

Throughout his early years as a cartoonist he mostly experimented with drawing on the darker side of his subconscious, basing his comedy on free-form association, much like the surrealist technique Automatism.

An example of such methods in Brown's work can be found in short one-pagers where he randomly selects comic panels from other sources and then mixes them up, often altering the dialogue.

In it, he puts forward the anti-psychiatric idea that what we call "schizophrenia" isn't a real disease at all, but instead a tool our society uses to deal with people who display socially unacceptable beliefs and behaviour.

Inspired by the evangelical tracts of Jack T. Chick, Brown left Xeroxes of these strips at bus stops and phone booths around Toronto so its message would reach a wider audience.

Despite drawing his panels individually, he says his "brain doesn't tend to think in terms of one image at a time", so that he has difficulty coming up with one-image covers.

Brown often talks of contemporaries Seth, Joe Matt and Julie Doucet's influence on his work, especially during his autobiographical period.

Underwater was originally intended to appear in Yummy Fur, but Brown's new publisher felt they could attract more readers with a different title.

[76][77] He has done the cover for Sook-Yin Lee's 1996 solo album Wigs 'n' Guns (to which he also contributed lyrics for one song),[78] and the poster for her film, Year of the Carnivore.

Brown was inducted into the Canadian Comic Book Creator Hall of Fame, on 18 June 2011, at the Joe Shuster Awards in Calgary, Alberta, Canada.