The Second Chechen War began in 1999 after attacks by Chechen forces on neighboring Dagestan and a series of terrorist attacks on residential buildings in Russian cities that caused more than 1000 casualties, which were blamed on Chechen terrorists.

In addition to a guerilla-style ground conflict within Chechnya, many terrorist attacks have happened which are attributed to Chechen terrorists by the Russian government. The Moscow Theatre Siege took place in October, 2002, when a group of Chechen terrorists held a crowded theater hostage for three days. On October 26, 2002, Russian special forces used an anaesthetic gas to disable the theatre's occupants, and inadvertently causing the deaths of many civilians through adverse reactions to the gas. This brought many questions and doubts about the policies of Russian President Vladimir Putin's strategy against Chechen terrorists. In December 2002, 2 truck bombs killed more than 70 people in the Chechen capital, Grozny and destroyed the headquarters of the pro-Moscow government.

According to Chechen rebel sources 60,000 civilians have so far died this war.

During the initial months of the war, Russia made effective use of air power instead of immediately rushing in massive numbers of ground troops. Thus, the Russians have avoided the first war's extremely high casualties. Russian forces later resorted to heavy carpet bombing and ballistic missile strikes against Grozny and other major cities. Though corridors were made for civilians to exit the cities when the attacks occurred, rebels sometimes blocked their escape. There are also reports of chemical weapons being used against rebels, though this is yet unconfirmed. Some Western countries have criticized heavy-handedness of the Russian military in dealing with the rebels, and both sides are charged with substantiated claims of torture, rape, looting, smuggling, and embezzlement.

In March 2002, the leader of the Fundamentalist Islamic rebel operations, Amir Khattab, was killed. Amir Abu al-Walid replaced him.

In December of 2002, a Russian court tried Russian Colonel Yuri Budanov on war crimes charges. He was accused of raping and strangling Heda Kungayeva, an 18 year old Chechen girl whom Budanov claims was a rebel sniper. In a controversial decision, he was found not guilty by reason of insanity on December 31, 2002 and committed to a psychiatric hospital for further evaluation and treatment.

Some Chechen terrorist leaders have repeatedly found refuge in various Western countries, to the great protest of Russia.

Despite public statements by Putin and other Russian officials insisting that the war is over, Chechen Islamist terrorists led by Shamil Basayev continue to wage a guerilla-style jihad against Russian troops and the Chechen administation, killing soldiers and civilians alike with frequent bombings, rocket, and gun attacks. Chechen rebels often videotape their work and publish the videos on the Internet.

See also: First Chechen War, Chechnya

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