Kovalyov has been an outspoken critic of authoritarian tendencies in the administrations of Boris Yeltsin and Vladimir Putin. In 1996, he resigned as head of Yeltsin's presidential human rights commission, having published an open letter to Yeltsin, where Kovalyov accused the president of giving up democratic principles. In 2002, he organized a public commission to investigate the 1999 Moscow apartment bombings (the Kovalyov Commission), which was effectively paralyzed after one of its members, Sergei Yushenkov, was assassinated, another member, Yuri Shchekochikhin, allegedly poisoned with thallium, and its legal counsel and investigator, Mikhail Trepashkin, arrested.