What is interesting in this case is the intersection of the world of espionage/assassinations with the world of anti-terrorism. Since 9/11, any act of political murder will be investigated much more strenuously because it might, just might, have been the act of one of those dastardly al-Quaedas... And nothing galvanizes public support like the threat of terror... But a consequence of all this new attention is that more political murders (which is to say those carried out agents working for traditionally governments) might come to light... Which of course causes problems when so called "allies" are secretly killing each others citizens.
But seriously, take a look at some of Litvinenko's accusations against Putin:
Blowing up Russia: Terror from Within, published in 2002 with the financial support of Berezovsky, Litvinenko alleged that agents from the FSB co-ordinated the 1999 apartment block bombings in Russia that killed more than 300 people. Russian officials blamed the explosions on Chechen separatists. In December 2003 Russian authorities confiscated over 4000 copies of the book en route to Moscow from the publisher in Latvia. In the book Gang from Lubyanka (Лубянская преступная группировка), Litvinenko alleged that Vladimir Putin during his time at FSB was personally involved in organized crime.
Litvinenko stated in a June 2003 interview, with the Australian SBS television program Dateline, that two of the Chechen terrorists involved in the 2002 Moscow theater siege — whom he named as "Abdul the Bloody" and "Abu Bakar" — were working for the FSB, and that the agency manipulated rebels into staging the attack. Litvinenko said: "[w]hen they tried to find [Abdul the Bloody and Abu Bakar] among the dead terrorists, they weren't there. The FSB got its agents out. So the FSB agents among Chechens organised the whole thing on FSB orders, and those agents were released." However, this theory has not been widely supported.
In a July 2005 interview with the Polish newspaper Rzeczpospolita, Litvinenko alleged that Ayman al-Zawahiri, along with other al-Qaeda leaders, was trained by the FSB in Dagestan (a republic neighboring Chechnya) in 1998.
In April 2006, a British MEP for London, Gerard Batten (UKIP), cited allegations by Litvinenko that Romano Prodi, the Italian Centre-Left leader (now Prime Minister) and former President of the European Commission, had been the KGB's "man in Italy". Batten demanded an inquiry into the allegations. He told the European Parliament that Litvinenko had been informed by FSB deputy chief, General Anatoly Trofimov (who was shot dead in Moscow in 2005,) that "Romano Prodi is our man (in Italy)". According to Brussels-based newspaper the EU Reporter on 3 April 2006, "another high-level source, a former KGB operative in London, has confirmed the story". Among Litvinenko's most serious claims is that Prodi assisted in the protection of KGB operatives allegedly involved in the assassination attempt on Pope John Paul II in 1981.
Okay, nothing at all damning there... Certainly not enough to Kill someone over... Right?