From the mid-1950s onwards, as a graduate student and a lecturer he opposed Trofim Lysenko's theories, then favored by Khrushchev and the ruling Communist Party of the Soviet Union.

[2][3]: 343  The 14 members of the group first drew public and international attention when they and 38 supporters signed an Appeal about political persecution in the USSR and sent it, over the head of the Soviet government, to the United Nations; meanwhile a number of them also became involved as authors and editors in the samizdat (self-published) human rights quarterly, the Chronicle of Current Events (1968–1983) which first appeared in April 1968.

After signing the May 1969 Appeal to the UN Human Rights Commission[6] Sergei Kovalyov went on to sign many statements and appeals, in defense of other dissidents, authors and rights activists: Vladimir Bukovsky, Mustafa Dzhemilev, Pyotr Grigorenko, Viktor Khaustov, Viktor Nekipelov, Leonid Plyushch, Yuri Shikhanovich, Aleksandr Solzhenitsyn and Gabriel Superfin.

He was arrested on 27 December 1974 in Moscow[9] and twelve months later he was put on trial in the Lithuanian capital Vilnius, charged with "anti-Soviet agitation and propaganda" .

The six years of reform initiated by the last Soviet leader Mikhail Gorbachev, often referred to as perestroika and glasnost, led to the release in 1987 of hundreds of political prisoners from the camps, from exile and from psychiatric hospitals,[11] and lifted residence restrictions from those who had completed their sentences.

[13] Its dual focus on the repressive Soviet past and the human rights issues of the present, made it particularly suitable for Kovalyov's involvement and he served as its co-chairman for many years after 1990.

Since 1994, Kovalyov, then Yeltsin's human rights adviser, has been publicly opposed to Russia's military involvement in Chechnya.

[15] Kovalyov has been an outspoken critic of authoritarian tendencies in the administrations of Boris Yeltsin and Vladimir Putin.

In 2002, he organized a public commission to investigate the 1999 Moscow apartment bombings (the Kovalyov Commission[16]), which was effectively paralyzed after one of its members, Sergei Yushenkov, was assassinated,[17][18] another member, Yuri Shchekochikhin, allegedly poisoned with thallium,[19][20] and its legal counsel and investigator, Mikhail Trepashkin, arrested.

In 2004, he was awarded the Victor Gollancz Prize by the Society for Threatened Peoples, for documenting Russian crimes in Chechnya.