One of the frequent counter-arguments employed by Christians against atheists who refer to the body counts racked up during the Crusades, the Inquisitions, and the Medieval pogroms against the Jews, to name a few examples, is to point out the millions of people who were killed by atheistic regimes such as Stalin's Soviet Union and Mao's Peoples' Republic of China.
To be fair, they do have a valid point. There are far greater forces for destruction in the world than religion, and the Soviet Union under Stalin is a perfect, if tragic, illustration of this fact. The truth is that it is not so much religion that is the problem as it is a matter of a totalitarian ideology that brooks no opposition or dissent, married to an overwhelming monopoly on force to carry out that ideology. That ideology can have either a religious or a secular basis.
But if one wants to hold up Stalin as a poster boy for the atrocities of atheism, one must also consider whether the blame should truly fall on atheism itself, or if instead if Stalin's atrocities were facilitated by a Russian culture that had historically been conditioned to obedience to absolutist dictators. In the case of Joseph Stalin, it is well known that the former seminarian was a great admirer of one of history's most notorious tyrants, Tsar Ivan the Fourth, better known as Ivan the Terrible.
Thus, if one wants to argue that atheism is at fault for the atrocities of Stalin's dictatorship, I would argue that one must ponder whether Stalin's murderous regime would have been possible if Russia had not first produced a tsar like Ivan the Terrible.