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A total of 42 episodes have been taken off the platform, some of which were removed in the last couple of weeks, according to Digital Music News.
Spotify is yet to share an explanation of the rationale behind the decision, but many of the discarded episodes feature controversial figures such as conspiracy theorist Alex Jones and the founder of far-right organisation Proud Boys, Gavin McInnes.
Rogan signed an extremely lucrative exclusivity deal with Spotify last year and he recently said he knew the streaming service wouldn't want every episode.
According to Digital Music News, the 53-year-old said: "There were a few episodes they didn't want on their platform, and I was like 'OK, I don't care'."
It's not clear though if he knew how many would be removed - or if the collection of episodes would be continually modified.
Announcing his deal with Spotify (reported to be worth $100 million) on Instagram last May, the presenter/MMA commentator/stand-up comedian said the show would be unchanged by the switch.
He said: "Announcement: the podcast is moving to @spotify! Starting on September 1 the podcast will be available on Spotify as well as all platforms, and then at the end of the year it will move exclusively to Spotify, including the video version.
"It will remain FREE, and it will be the exact same show. It's just a licensing deal, so Spotify won't have any creative control over the show. They want me to just continue doing it the way I'm doing it right now."
He continued: "We will still have clips up on YouTube but full versions of the show will only be on Spotify after the end of the year.
"I'm excited to have the support of the largest audio platform in the world and I hope you folks are there when we make the switch!"
Yeah, reckon I'd probs be pretty excited to have $100 million worth of support too. No wonder he doesn't care about episodes being removed, and to be honest, we've all still got more than 1,600 episodes to choose from.
LADbible has contacted Spotify for comment.
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