Hughes died on Monday in hospital aged 51, a representative for the comedian, actor and writer confirmed.
The comedian was believed to have been suffering from cirrhosis of the liver and died in London's Whittington Hospital.
Hughes was best known for his appearances on Never Mind the Buzzcocks and his own sitcom Sean's Show.
In a varied career, Hughes also had acting roles in The Commitments Coronation Street, and Agatha Christie's Marple.
He was also a team captain on the BBC 2 comedy quiz show Never Mind the Buzzcocks, from 1996 to 2002, alongside Phill Jupitus and Mark Lamarr.
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Hughes was a familiar face on television with Sean's Show on Channel 4 in 1922. Very talented comic, loved & respected.
Matt continued: 'He'd been unwell, but when I started out on the comedy circuit about 25 years ago, Sean was one of the biggest stars'.
Comedian Jason Manford was among one of the first to pay tribute to Hughes, writing on Twitter: "Very sad to hear about Sean Hughes".
"I am a huge fan of his and am very sad to hear this news".
Irish comedian Aisling Bea tweeted, "So sad".
Sean leaves behind his mum and two brothers.