Born in Milan, he has a degree in economics from the Bocconi University in Italy. He was the general advisor of the "Movement of the Pannella Club" from 1994 to 1995, when he was appointed national secretary of the Movement and of the General Council of the Transnational Radical Party.
After a brief experience in the field of human resource management at the Galbani de Melzo Institute, he started to collaborate with the radical group within the European Parliament in 1995. In 1996 he was appointed treasurer of the CORA (Radical Antiprohibitionist coordinator). In 1997 and 1998 he was the Transnational Radical Party representative at the United Nations in New York, where he became particularly involved in the campaign for the implementation of the International Criminal Court. From February 1999 to July 2001 he was Coordinator to the "Radical Committee for the liberal revolution of the United States of Europe". From June 1999 to July 2004 he was a MEP representing the Lista Bonino.
He was the European Parliament "rapporteur" on the Directive on "privacy with regard to electronic communication".
Due to his efforts in countering the generalized control proposals in the field of electronic communications (he is mostly known for his report on privacy in electronic communications) he was awarded the European of the Year title by the weekly newspaper "European Voice". The citation stated that the award was "for his leadership in the campaign for the protection of privacy, in particular in respect of the preservation of the protection of the citizens personal data in the very moment where the United States have undertaken a war against terrorism." Cappato however donated the 5,000 euro award to the Luca Coscioni Association for the freedom of scientific research.
Furthermore, he was nominated for the "Politician of the Year" award - for his campaigning against European monitoring laws- by the American magazine "Wired". In December 2001 he was arrested in Manchester for a non-violent action of civil disobedience in connection with the British laws against possession of drugs for personal use.
From March to November 2002 he was the president of the Transnational Radical Party board. Since October 2002 he has been the coordinator of the Parliamentarians for Antiprohibitionist Action (PAA) a group which has received the support of about 200 parliamentarians from all around the world.
Secretary of the Luca Coscioni Association for Freedom of Research since January 2004. Co-ordinator of the electoral and referendum initiatives of the radical and radical-liberal area for the 2004 European elections.
In 2004 he is elected Secretary of the 'Luca Coscioni Association for Freedom of Scientific Research "; he is one of the promoters of the committees for referendum for the cancellation of the new law on assisted reproduction and coordinator of the referendum and electoral initiatives of the radical-liberal area for the European elections of 2004. After the encounter with Luca Coscioni, the university researcher sick of amyotrophic lateral sclerosis, who invests the party with a campaign for freedom of scientific research, Cappato also deals directly with the issue. During his parliamentary mandate he is committed to successfully unlock the European funds for research on stem cells from supernumerary embryos. As Secretary of the 'Luca Coscioni Association for Freedom of Scientific Research ", Cappato is among the promoters of the constitutive session of the World Congress for Freedom of scientific research." In 2005 he is re-elected Secretary of the Luca Coscioni Association, which helps to constitute the new entity of the new liberal-socialist political subject of the Rose in the Fist. He is elected to the Lower House in the election of 9 and 10 of April for the Piemonte region I. On 8 May 2006 has resigns to go to cover the functions of MEP, to succeeded to Emma Bonino. In the European Parliament he enters in the Group of the Alliance of Liberals and Democrats for Europe. He is a member of the Committee on Foreign Affairs and the Delegation for relations with the Mashrek countries. On 27 May 2007 he is arrested in Moscow while he was at the head of a delegation from the Radical Party, together with parliamentarians from other groups, who wanted to deliver to Mayor Luzhkov a letter signed by 50 MEPs who called the authorities to authorize the holding of the Gay Moscow pride. While the flier was distributed with the text of the letter, a group of naziskin violently attacked the demonstrators. Soon after there was intervention by the Russian police, rather than protect the victims, took steps to arrest them. He was released the next day without trial, although he had asked to be submitted and for which he also produced a 'articulate defense. On 19 December 2008 Marco Cappato, together with Antonella Casu (Secretary of the Italian Radicals), and Sergio D'Elia (Secretary of Hands Off Cain), submitted the complaint to the Labor Minister Maurizio Sacconi, at the Public Prosecutor of Rome, for private violence and intimidation, , following the his address of a few days before on the issue of Eluana Englaro.
On 14 January 2009 his report of the European Parliament on access to documents of the European Council, the European Parliament and European Commission is approved in Strasbourg (with 355 votes in favor and 195 against). In particular, proposals borrowed from the Italian Radical Party for a public registry of the elect, against absenteeism of Italian MEPs and European have been approved. On 17 January 2009, following its complaint, the Public Prosecutor of Rome include the Minister Maurizio Sacconi to the register of suspects.
In the spring of 2009, he ran for the elections for European Parliament for the Lista Emma Bonino but he was not elected.