However, there were gay "jokes" from the beginning. In a running gag, Brain has a sudden insight and asks Pinky "Are you pondering what I'm pondering?" Pinky replies with a nonsequiter that can often be read as sexual, or at least dirty, such as "I think so, Brain, but how can we get seven dwarves to shave their legs?" or "I think so, Brain, but isn't a cucumber that small called a gherkin?"
Of seventy-five recorded "pondering" responses, thirteen concern transvestism or fetish costumes — "I think so, Brain, but this time you wear the tutu" — and twelve evoke sexual double entendres — "I think so, Brain, but apply North Pole to what?"
The tag line of each episode, after the most recent plan for world domination has failed, similarly allows for a homoerotic reading:
Brain: Let us go back to the lab and prepare for tomorrow night.
Pinky: Why, Brain? What are we going to do tomorrow night?
Brain: The same thing we do every night, Pinky. [Pause, while we ponder just what it is that they do every night] Try to take over the world.
When Pinky and the Brain moved to prime time in 1995, plotlines became more complex, with movie and television parodies and recreations of the basic scenario in various historic periods. The writers also added what Warner Brother's head of programming referred to as "family and romantic element." Potential heterosexual partners did appear occasionally, and Brain was somewhat swayable, but Pinky steadfastly chose the Brain over any other love.
Most of the romantic elements, however, involved the duo's attraction to each other, which Pinky celebrated and the Brain grudgingly admitted. In "Just Say Narf", Pinky sings and flirts with a despondent Brain: he bats his eyes seductively, lays his head cozily in Brain's lap, and twirls him about in a waltz before Brain finally cheers up.
Even when the Brain takes up smoking, Pinky's attraction does not diminish: "Hello there, stinky smelly smoky boy," he says with a leer, "Do you have a monkey in your pants?" He "means" to say "Do you have a monkey on your back?", a metaphor for addiction. When he says "pants" instead, the "mistake" produces a striking metaphor that is not not sexual.
Pinky and the Brain share more than physical attraction, however; they begin to represent themselves as a closeted gay couple. A prospective employer asks Brain, "Are you married?" After a brief, awkward pause, he responds "No. I do have a ... roommate." Considering various responses and then deciding on "roommate" is — or was — a familiar strategy for hiding same-sex partners from potential homophobes. Brain gets the job and enters corporate culture as a closeted gay man — or mouse — clumsily rejecting a female suitor and inventing a lame explanation for the picture of Pinky on his desk.
When Brain's parents visit, Brain again introduces Pinky as "my ... um ... roommate." The liberated 1990's parents are not fooled, however; while constantly criticizing Brain for his poor housekeeping, poor cooking, and unrealistic career goals, they never nag him to "meet a nice girl" and get married; obviously they are aware that he already has a partner. At the end of the episode, Mom and Dad invite the two to visit as a couple at Thanksgiving.
No other cartoon of the 1990's portrayed same-sex relationships so overtly.