Human rights violations were committed by the warring sides during the second war in Chechnya. Both Russian officials and Chechen rebels have been regularly and repeatedly accused of committing war crimes including kidnapping, torture, murder, hostage taking, looting, rape, decapitation, and assorted other breaches of the law of war. International and humanitarian organizations, including the Council of Europe and Amnesty International, have criticized both sides of the conflict for blatant and sustained violations of international humanitarian law.

Crimes Forced disappearances Human rights campaigners estimate that since September 1999 – the start of the second Chechen conflict – as many as 5,000 people have disappeared and are feared dead.Russia censured over Chechen man BBC According to Amnesty International in 2005, Russian officials give about 2,000 as the official figure for "disappearances" since late 1999.

In March 2001 Human Rights Watch (HRW) issued the report titled The "Dirty War" In Chechnya, which called the "disappearances" of detainees in the custody of Russian federal forces in Chechnya a major human rights crisis that the international community must address. On February 25–26, 2006, Alvaro Gil-Robles, resigning Council of Europe's Commissioner for Human Rights, visited Chechnya, together with his successor, Thomas Hammarberg ; they criticized abductions, impunity and lack of security in Chechnya. On March 2, 2006, Chechen ombudsman Nurdi Nukhadzhiyev stated the problem of forced disappearances of people in Chechnya cannot be solved by local authorities, adding that a special commission has to be created at federal level. On May 12, 2006, Dmitry Grushkin of the 'Memorial' human rights group told Interfax that at least 1,893 residents of Chechnya had been kidnapped since 2002; of those, he said, 653 were found alive, 186 were found dead, and 1,023 "disappeared". 'Memorial' monitors kidnappings for only 25-30 percent of Chechen territory. On November 13, 2006, HRW published a briefing paper on torture in Chechnya that it had prepared for the 37th session of the United Nations Committee Against Torture. The paper covered torture by personnel of the Second Operational Investigative Bureau (ORB-2), torture by units under the effective command of Ramzan Kadyrov, torture in secret detention and continuing "disappearances." According to HRW, torture "in both official and secret detention facilities is widespread and systematic in Chechnya. Based on extensive research, HRW concluded in 2005 that forced disappearances in Chechnya are so widespread and systematic that they constitute crime against humanity."

Mass hostage takings

Moscow theater hostage crisis

On October 23, 2002, over 40 terrorists took more than 700 hostages prisoner at a Moscow theater. The hostage-takers demanded an end to the Russian presence in Chechnya, and threatened to execute the hostages if their conditions were not met. The siege ended violently on October 26, when Russian troops were forced to storm the building after the detonation of some explosive devices inside. Many casualties resulted from the fact that unconscious victims' airways were blocked and sub-optimal care was given during the rescue. In particular, the failure of Russian authorities to equip their troops with opioid antidotes and their efforts to conceal the identity of the gas for days afterward hindered efforts to save the lives of the stricken hostages.

On November 2, Shamil Basayev assumed responsibility for the attack and apologized to Aslan Maskhadov for not informing him of the plan.

Beslan school siege

On September 1, 2004, a group of 32 heavily armed, masked men seized control of Middle School Number One and more than 1,000 hostages in Beslan, North Ossetia. Most of the hostages were children aged from six to sixteen years old. Following a tense two-day standoff punctuated by occasional gunfire and explosions, Alpha Group of the FSB raided the building. The fighting lasted more than two hours; ultimately 331 civilians, 11 commandos and 31 hostage-takers died.

Russian officials publicly linked Basayev and Maskhadov to the attack. Basayev claimed responsibility in a September 17 website publication; Maskhadov denounced the attacks and denied involvement. The carnage at Beslan and the outcry it caused has had an unexpected effect on the tactics employed by Chechen separatists and their allies.

Other hostage incidents March 15, 2001 – three Chechens hijacked a Russian Tu-154 aircraft with 174 people on board after it left Turkey; they forced it to land in Medina, Saudi Arabia. On March 16, Saudi commandos freed over 100 hostages, killing three people including a hijacker, a female flight attendant and a Turkish passenger. A Russian diplomat in Saudi Arabia said the leader of the hijackers was a "highly-trained military officer who appears to know what he is doing." April 22, 2001 – in Turkey pro-Chechen gunmen seized up to 100 hostages at a luxury hotel in Istanbul. The standoff lasted nearly 12 hours before the hostage-takers, armed with automatic rifles, surrendered; police said they had encountered no resistance from the gunmen and there were no reports of anybody being injured.

October 29, 2004 – the State Duma hosted Vladimir Ustinov, head of the Prosecutor General's Office, to discuss the Putin administration's anti-terrorism strategy. As he explained it to the deputies, in future hostage-taking episodes the security agencies would have a formal statutory right to seize and detain the relatives of the suspected hostage-takers. The government would then let the terrorists know that it will do to these "counter-hostages" whatever the terrorists do to their own hostages.

Meanwhile, the practice of taking civilians hostages exists among the officers of Russian and local security agencies in Chechnya. On March 1, 2004, officers of security agencies seized more than 30 relatives of former Ichkerian defence minister Magomed Khambiyev, including women, in the Khambiyev family's native village of Benoy in Chechnya's Nozhay-Yurtovsky District. Magomed Khambiyev got an ultimatum to lay down his arms in exchange for the lives of his relatives; he did it, giving himself up to the authorities in a few days.

June 3, 2006 – Russian diplomats in Iraq were seized when their convoy was waylaid by the Mujahedeen Shura Council. One was shot during the kidnapping; three others were later executed. The group hoped to pressure Russia into allowing Chechnya to secede and become an Islamic theocracy.

Massacres

Indiscriminate attacks On October 5, 1999, a bus filled with refugees was reportedly hit by a Russian tank shell, killing as many as 40 civilians and wounding several others. On October 7, 1999, federal forces carried out a cluster bomb attack on the village of Elistanzhy in Vedensky District. Within several minutes 27 people were killed; among them only eight were men of "fighting age", meaning aged 14 to 60. In the next two weeks, 21 more died of their wounds. On October 21, 1999, a series of Russian ballistic missile strikes on central Grozny killed at least 137 people, mostly civilians, and injured hundreds. The missiles hit the city's main marketplace, a maternity hospital and a mosque. On October 24, 1999, seven children were killed and 14 maimed by a Russian tank attack in Novy Sharoy; an adult man was also killed. On October 29, 1999, the Russian Air Force carried out a rocket attack on a large convoy of refugees who were using a "safe exit" route. Casualties were estimated at 50-100, among them several Red Cross workers, two journalists and many women and children. On February 4, 2000, in an attempt to stop the Chechen retreat, Russian forces bombed the village of Katyr-Yurt, then a civilian convoy under white flags, killing at least 170 civilians, while many more were injured. On February 9, 2000, a Russian tactical missile hit a crowd of people who had come to the local administration building in Shali, a town declared to be one of the "safe areas", to collect their pensions. The missile is estimated to have killed some 150 civilians, and was followed by an attack by combat helicopters causing further casualties. The Russian attack, which happened without any warning, was a response to infiltration of the town by a group of Chechen fighters who suffered few casualties.

Documented mass killings On December 3, 1999, at least 40 people fleeing the besieged Grozny were shot and killed by Russian troops, leaving only seven wounded survivors. In early December 1999, Russian troops under the command of General Vladimir Shamanov killed up to 41 civilians during a two-week drunken rampage in the village of Alkhan-Yurt, near Grozny. In several incidents during December 1999 and January 2000 in the Staropromyslovski district of Grozny, Russian troops killed at least 50 unarmed civilians, mostly elderly men and women. A particularly brutal massacre was carried out on February 5, 2000 in the suburb of Novye Aldi, where suspected members of OMON, a special purpose police unit from St Petersburg and contract soldiers summarily executed at least 60 civilians. Following the March 2000 Battle of Komsomolskoye about 70 Chechen combatants who were taken prisoner were officially amnestied, but almost all of them are believed to have been murdered in captivity. From 1999 to 2004, the Chernokozovo detention center operated as a filtration and torture camp, and human rights abuses were documented in the facility.

Rebel bombings September 6–14, 1999 – a series of nighttime explosions in apartment buildings using hexogen (RDX) killed 307 and injured 1,700 people. Four buildings in Moscow, Buinaksk and Volgodonsk were destroyed. (Disputed – Evidence points to a russian false flag operation.) May 9, 2002 – an explosion of a Russian-made anti-personnel mine in the Dagestani town of Kaspiysk killed 45 and wounded some 175 soldiers and civilian bystanders during a military parade. A Dagestani pro-Chechen group blamed for an attack had previously killed seven Russian soldiers on January 18, 2001, in the Dagestani capital, Makhachkala. June 12, 2005 – a bomb planted by Russian nationalist extremists, said to be veterans of the Chechen wars belonging to the Russian National Unity group, derailed the Grozny-Moscow passenger train some 150 kilometers south of the Russian capital. Dozens of people were injured, but only eight hospitalized. On May 30, 2006, suspects Vladimir Vlasov and Mikhail Klevachyov were charged with terrorism and attempting to commit murder motivated by ethnic or religious hatred.

Suicide bombings

Between June 2000 and September 2004, Chechen insurgents added suicide attacks to their weaponry. During this period there were 23 Chechen related suicide attacks in and outside Chechnya, targeting both military and civilian targets, the profiles of the suicide bombers have varied just as much as the circumstances surrounding the bombings. Although only six of the attacks were directed against civilians, these attacks have drawn the lion's share of the publicity generated by Chechen suicide tactics.

July 5, 2003 – 19-year-old Zulichan Elichadzjijeva blew herself up outside a rock festival at the Tushino airfield near Moscow. Her bomb did not detonate as expected. 15 minutes later, only a few meters from the site of the first attack, 26-year-old Zinaida Alijeva detonated her explosives and killed 11 people instantly. Four more died in hospital. For many observers, the Tushino attacks appeared out of place.