Stonestreet, 41, who picked up an Emmy for outstanding supporting actor in a comedy on Monday, recently split from his long-term girlfriend, Broadway actress Katherine Tokarz.
Theron, on the other hand, has been flying solo since she casually dated Ryan Reynolds just before he started seeing his now-wife Blake Lively in 2011. Prior to that, she was in a relationship with actor Stuart Townsend for nine years. They split in 2010.
The actress adopted a baby boy named Jackson in March.
But here's the rub with the new romance reports - the funnyman's rep says they're hogwash.
"There is nothing romantic going on between them. He has only met Charlize twice!" Stonestreet's rep told People.
On one of those occasions they were snapped together at the White House Correspondents' Dinner in April.
'IT'S STARTING TO MAKE HALLE BERRY JEALOUS'
Stonestreet also took to Twitter to weigh in on the rumour.
"I wish people would stop spreading rumours that Charlize Theron and I are dating. It's starting to make Halle Berry jealous," he quipped.
The actor also joked about the rumour on the Emmy Awards red carpet.
"She [Halle Berry] was so cold to me this morning when she saw these rumours," he said. "It was just quiet - fork and knife on the plate. Halle and I weren't speaking at all. And I'm like, 'Halle, listen! It's just a rumour. It's not real.'"
Stonestreet added that he "would love to know" why he's been romantically linked to Theron.
"For all of you watching at home, that's the definition of our town, that I'm rumoured to be dating Charlize Theron."
Snow White and the Huntsman star Theron dished in May that she was relishing her new role as a mother.
"I love it! I've got to tell you, I'm available for other babies' diapers to be changed. I can do it in my sleep now. I am so good," she told The Today Show. "I now know how to change a Japanese diaper, a Spanish diaper, an English diaper, a German diaper. I'm like the diaper pro now."
She added: "The one thing I'm grateful beyond anything else is that she [her mother Gerda] raised me to always encourage me to be my own person... and that teaches great independence and confidence.
"And I would hope to have my son feel the same way about himself. And kind of go and discover the world in his own skin."
FAST GOSSIP
And finally...
* I won't have what he's having: Bad hair day, Mickey Rourke?
* Lady Gaga's former PA claims her demands for privacy are "ludicrous".
* Rekindled romance: Zoe Saldana and Bradley Cooper are back on.
* Natalie Portman goes blonde, hangs out with Robert Pattinson.
* Total recall: Arnold Schwarzenegger confessed to his wife Maria Shriver about his love child at a marriage therapy session. "The minute we sat down, the therapist turned to me and said, 'Maria wanted to come here today and to ask about a child - whether you fathered a child with your housekeeper Mildred'," Schwarzenegger writes in his new tell-all. "I told the therapist, 'It's true'." Shriver filed for divorce in July 2011.
* Kanye West's lawyer sends cease and desist letter to website over sex tapes (there's two being shopped, apparently).
* James Franco, rock star? The jack of all trades adds musician to his lengthy resume.
* Justin Bieber gives his wheels to Sean Kingston.
* First official image of (shirtless) Hugh Jackman in The Wolverine.
* Teaser trailer: Lindsay Lohan as legendary silver screen star Elizabeth Taylor in Lifetime's upcoming biopic, Liz & Dick:
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