Forget about tech woes and the tea party, Obamacare's biggest headache might be Jon Stewart.
"The Daily Show" host put Health and Human Services Secretary Kathleen Sebelius on his comedic hotseat Monday night, teasing her about how very, very, very slow her federal online health insurance marketplace has been since launching last week.
"We're gonna do a challenge," Stewart said. "I'm gonna try to download every movie ever made, and you're going to try to sign up for Obamacare and we'll see what happens first," he said to big laughs from his Comedy Central audience.
Before Sebelius trotted out for her good-natured ribbing, Stewart lampooned the hyperbolic fears of Obamacare by congressional Republicans, the technologically hobbled roll-out of the the federal marketplace and Americans' refusal to be patient with the new law.
"Obamacare has exploded the chest cavities of millions of Americans," Stewart said, as he played a clip showing the infamous exploding chest scene from the film "Alien."
"We will camp out all night to be the first people to buy a phone or see a movie about shirtless werewolves, but you have 10 minutes to get me this [expletive] health care!"
(Read more: Obamacare tech headaches)
Stewart said President Barack Obama's failure to make sure the Healthcare.gov was ready to handle the flood of visitors "would be like if Lincoln didn't end up proofreading the Emancipation Proclamation and ended up freeing all the 'daves.'"
When Sebelius came out, Stewart asked about enrollment in the Obamacare insurance plans, which by all accounts have been a tiny fraction of the 7 million or so Sebelius' department is aiming for.
"How many have signed up this far?" Stewart asked.
"I can't tell you," Sebelius said. "Because I don't know."
Despite the easy laughs he got for joking about the technological glitches, Stewart seriously—and repeatedly—pressed Sebelius to explain why the Obama administration delayed by one year the requirement that medium- and large-sized employers provide health coverage to their workers, but gave individuals no such reprieve from having insurance by 2014 or facing a tax penalty.
"If I'm an individual....who doesn't want it," Stewart said, "it would be hard for me to look at big business getting a waiver and not having to do it, and me having to. ... It looks like because I don't have a lobbying group."
(Read more: Conquering the glitches)
Sebelius gamely tried to answer his pointed questions, noting that the vast majority of bigger employers already provide insurance, and that government subsidies are going to be available for many individuals to help buy insurance.
"Oh, so you're doing it because you haven't been able to get the subsidies ready for business?" Stewart asked.
"Well," Sebelius said, "The businesses don't get any subsidies."
Stewart, seemingly trying to follow the rationale, said, "So, they get to delay because they're not going to get any extra money, but individuals don't because they will?"
Stewart then said, to laughs, "Let me ask you this: Am I a stupid man?"
He concluded by asking, again in all seriousness, why Obamacare was tackling the issue of health-care reform by using a market-based solution of compelling nearly all Americans to purchase health insurance, instead of implementing a "single-payer" system where health coverage was provided by the government.
(Read more: Obamacare rollout begins)
"I honestly don't understand why businesses wouldn't jump at the chance to decouple health insurance from their responsibility, and why the government wouldn't jump at the chance to create a single-payer system that is simplifying this garbledy-gook and create the program I think America deserves," Stewart said to big applause from the audience.
Sebelius ironically replied, "As you know, we're facing the end of Western Civilization by having a market-based strategy."
But before she could explain why a single-payer system would have had little chance overcoming Republican opposition, Stewart cut to the chase.
"This is a system that has been jerry-rigged to deal with the crazy people," he said.
—By CNBC's Dan Mangan. Follow him on Twitter @_DanMangan.