The US radio giant said it was axing Stern from its stations under a new "zero tolerance" policy toward indecency. Stern's fall comes hot on the heels of an interview with Rick Salomon, who is now infamous for releasing a movie of himself having sex with heiress Paris Hilton.
In the interview Stern asks Salomon if he had anal sex with Hilton and asked him about the size of his penis. Clear Channel said the show crossed the line.
In a statement Clear Channel Radio president John Hogan said: "Clear Channel drew a line in the sand today with regard to protecting our listeners from indecent content and Howard Stern's show blew right through it.
"It was vulgar, offensive and insulting, not just to women and African Americans but to anyone with a sense of common decency."
The axing of Stern follows Clear Channel firing a Florida radio personality "Bubba the Love Sponge" after he was accused of airing sexually graphic material.
Stern's show was carried on six of Clear Channel's stations. However, the radio waves will not get off that lightly. Stern's New York-based show is syndicated through Viacom subsidiary Infinity Broadcasting, which operates 185 radio stations in the US.
Infinity has made no comment but Viacom president Mel Karmazin was recently reported as saying that "this company won't be a poster child for indecency."
Since Janet Jackson exposed her breast at the Super Bowl on February 1 there has been uproar across the US.
Earlier this week Jackson lost her role in a TV movie biography about singer Lena Horne after Horne complained to ABC.
US communications regulator the FCC and Congress have both used the Jackson nipple incident as incitement to impose new restrictions on television and cable networks.
It appears that US lawmakers could pass legislation leading to a tenfold increase in the fine on television and radio broadcasters that violate FCC decency rules, equalling $275,000 per violation.
There is even cross-party talk of a "three strikes and you're off the air" law that could see the FCC take back licences of repeat offenders.
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