His shows have always been criticized for the leftism and lack of impartiality like in the last years with attacks against Berlusconi and other right wing Italian MPs.

In recent years he has been continually accused of partisanship by the right-wing coalition House of Freedoms led by Berlusconi, whose family holding company controls Mediaset, who installed a new board in the state-owned RAI after their electoral victory in the 2001 Italian general election.

This followed a declaration by Silvio Berlusconi, then prime minister of Italy, at a press conference in Sofia, Bulgaria, where he stated: "Santoro, Biagi and Luttazzi used the public TV, paid by all, in a manner which is criminal.

He was supported by a court decision that should have forced RAI to give him the direction of a news magazine,[3] but in the end Santoro was omitted.

In the 2004 European elections, Santoro accepted the offer of candidacy proposed by the centre-left confederation called United in the Olive Tree.

Michele Santoro resigned as an MEP on 19 October 2005, basing his decision on his desire to go back to his work on RAI, citing a judicial verdict which obliged the Italian national television to reinstate him.

The episode of the show aired on 8 March 2007, which featured Italian Minister of Justice Clemente Mastella as special guest, caused controversy for his strong position on the DiCo issue.