Atrocity crimes in the Soviet–Afghan War were systematically perpetrated on a large scale by the Soviet Union and its allies from 1979 to 1989, with several scholars and academics concluding that the Soviet military forces carried out a campaign of genocide against Afghans.; ; ; ; The war resulted in the deaths of between 1,000,000 and 3,000,000 Afghans. Estimates of Afghan civilian deaths vary from 562,000 to 2,000,000. Human Rights Watch concluded that the Soviet Red Army and the Afghan Army perpetrated war crimes and crimes against humanity in Afghanistan, intentionally targeting civilians and civilian areas for attack, and killing and torturing prisoners.

Pre-invasion repression Afghan president Mohammed Daoud Khan was deposed and murdered in 1978's Saur Revolution by the Khalqist faction of People's Democratic Party of Afghanistan (PDPA), who subsequently established their own government, the Democratic Republic of Afghanistan. Political scientist Barnett Rubin wrote, "Khalq used mass arrests, torture, and secret executions on a scale Afghanistan had not seen since the time of Abdur Rahman Khan, and probably not even then". After gaining power, the Khalqists unleashed a campaign of "red terror", killing more than 27,000 people in the Pul-e-Charkhi prison, prior to the Soviet invasion of Afghanistan in December 1979. Political scientist Olivier Roy estimated between 50,000 and 100,000 people disappeared during the Taraki–Amin period.

Crimes After Soviet Union invaded Afghanistan, deposing and killing Hafizullah Amin in Operation Storm-333 and installing Babrak Karmal as General Secretary, the brutality of communists intensified. The army of the Soviet Union killed large numbers of Afghans, attempting to suppress resistance from the Afghan mujahideen. Numerous mass murders were perpetrated by the Soviet Army during the summer of 1980.:"Incidents of the mass killing of noncombatant civilians were observed in the summer of 1980...the Soviets felt it necessary to suppress defenseless civilians by killing them indiscriminately, by compelling them to flee abroad, and by destroying their crops and means of irrigation, the basis of their livelihood. The dropping of booby traps from the air, the planting of mines, and the use of chemical substances, though not on a wide scale, were also meant to serve the same purpose...they undertook military operations in an effort to ensure speedy submission: hence the wide use of aerial weapons, in particular helicopter gunships or the kind of inaccurate weapons that cannot discriminate between combatants and noncombatants." Soviet forces also launched chemical attacks against civilian populations. During the 1980s, the communist PDPA regime also killed and tortured thousands of individuals in the Pul-e-Charkhi prison.

Murder, willful killings, massacres

Several massacres were reported by the Soviet Army. In the September 1982 Padkhwab-e Shana massacre, the Soviet Army threw a mix of gasoline, pentrite and trinitrotoluene inside a qanat where locals were hiding, and then ignited an explosion, killing them. 105 people were killed in the crime, including children, old people and combatants. In the October 1983 Kulchabat, Bala Karz and Mushkizi massacre, up to 360 people were gathered at the three village squares and shot, including 20 girls and over a dozen older people. In March 1984, a hundred civilians were massacred in two villages in the Kohistanat District; Dash-e-Bolokhan and Dash-e-Sulukhan; while 40 civilians were killed in Zirvq village, Urgun District, in November 1984. In the December 1984 Kunduz massacre, in the village of Haji Rahmatullah in the Kunduz Province, around 250 civilians were reportedly killed in what was described as Soviet reprisals against civilians for anti-communist resistance members and their military actions aimed against the Soviet Army. In April 1985, in the Laghman massacre in the villages of Kas-Aziz-Khan, Charbagh, Bala Bagh, Sabzabad, Mamdrawer, Haider Khan and Pul-i-Joghi in the Laghman Province, between 500 and 1,000 civilians were murdered in what was described as Soviet reprisals against civilians for anti-communist resistance members and their military actions aimed against the Soviet Army.

The army of the Soviet Union killed large numbers of Afghans to suppress their resistance. In one notable incident the Soviet Army committed mass killing of civilians in the summer of 1980. To separate the Mujahideen from the local populations and eliminate their support, the Soviet army killed many civilians, drove many more Afghans from their homes, and used scorched-earth tactics to prevent their return. They used booby traps, mines, and chemical substances throughout the country. The Soviet army indiscriminately killed combatants and non-combatants to terrorize local populations into submission. The provinces of Nangarhar, Ghazni, Laghman, Kunar, Zabul, Kandahar, Badakhshan, Logar, Paktia and Paktika witnessed extensive depopulation programmes by the Soviet forces.

Overall, between 6.5 and 11.5% of Afghanistan's population is estimated to have perished in the war. Anti-government forces were also responsible for some casualties. Rocket attacks on Kabul's residential areas caused more than 4,000 civilian deaths in 1987 according to the UN's Ermacora.Sandy Gall. Afghanistan: Agony of a Nation. Bodley Head. 1988 p. 3 Scholar Antonio Giustozzi estimates 150,000 to 180,000 mujahedeen casualties, of which half of them died. He also puts the fatalities of the communist-allied Democratic Republic of Afghanistan at over 58,000 by 1989.

Rape The Soviet forces abducted Afghan women in helicopters while flying in the country in search of Mujahideen. In November 1980 a number of such incidents had taken place in various parts of the country, including Laghman and Kama. Soviet soldiers as well as KhAD agents kidnapped young women from the city of Kabul and the areas of Darul Aman and Khair Khana, near the Soviet garrisons, to rape them.: "While military operations in the country were going on, women were abducted. While flying in the country in search of mujahideen, helicopters would land in fields where women were spotted. While Afghan women do mainly domestic chores, they also work in fields assisting their husbands or performing tasks by themselves. The women were now exposed to the Soviets, who kidnapped them with helicopters. By November 1980 a number of such incidents had taken place in various parts of the country, including Laghman and Kama. In the city of Kabul, too, the Soviets kidnapped women, taking them away in tanks and other vehicles, especially after dark. Such incidents happened mainly in the areas of Darul Aman and Khair Khana, near the Soviet garrisons. At times such acts were committed even during the day. KhAD agents also did the same. Small groups of them would pick up young women in the streets, apparently to question them but in reality to satisfy their lust: in the name of security, they had the power to commit excesses." Women who were taken and raped by Soviet soldiers were considered 'dishonoured' by their families if they returned home. Deserters from the Soviet Army in 1984 also reported the atrocities by Soviet troops on Afghan women and children, including rape.

Indiscriminate attacks and bombardments 46% of all Afghan fatalities were killed by Soviet bombardments of cities and villages, amounting to 400,000 civilian deaths, meaning that, on average, 26 civilians were killed per each killed Soviet soldier. In one case in October 1984, 300 families fleeing to Pakistan were bombed by Soviet forces in Chaghcharan, Ghor Province. Hospitals were bombed in 1981 in Ostoma, and again in 1982 and 1984. Some of the hospitals removed their insignia of the Red Cross to avoid being the target of the Soviet Air Force.

Scorched-earth tactics and wanton destruction

Irrigation systems, crucial to agriculture in Afghanistan's arid climate, were destroyed by aerial bombing and strafing by Soviet or government forces. In the worst year of the war, 1985, well over half of all the farmers who remained in Afghanistan had their fields bombed, and over one quarter had their irrigation systems destroyed and their livestock shot by Soviet or government troops, according to a survey conducted by Swedish relief experts.

The scorched-earth strategy implemented by the Soviet Air Force consisted of carpet bombing of cities and indiscriminate bombings that destroyed entire villages. Millions of land-mines were planted by Soviet military across Afghanistan. Around 90% of Kandahar's inhabitants were de-populated, as a result of Soviet atrocities during the war.

Everything was the target in the country, from cities, villages, up to schools, hospitals, roads, bridges, factories and orchards. Soviet tactics included targeting areas which showed support for the Mujahideen, and forcing the populace to flee the rural territories the communists were unable to control. Half of Afghanistan's 24,000 villages were destroyed by the end of the war. Rosanne Klass compared the extermination campaigns of the Soviet military to the carnage unleashed during the Mongol invasion of Afghanistan in the 13th century.

The population of Afghanistan's second largest city, Kandahar, was reduced from 200,000 before the war to no more than 25,000 inhabitants, following a months-long campaign of carpet bombing and bulldozing by the Soviets and Afghan communist soldiers in 1987. Land mines had killed 25,000 Afghans during the war and another 10–15 million land mines, most planted by Soviet and government forces, were left scattered throughout the countryside. The International Committee of the Red Cross estimated in 1994 that it would take 4,300 years to remove all the Soviet land mines in Afghanistan, which continued to kill hundreds of people on yearly basis.

A great deal of damage was done to the civilian children population by land mines. A 2005 report estimated 3–4% of the Afghan population were disabled due to Soviet and government land mines. In the city of Quetta, a survey of refugee women and children taken shortly after the Soviet withdrawal found child mortality at 31%, and over 80% of the children refugees to be unregistered. Of children who survived, 67% were severely malnourished, with malnutrition increasing with age.

Forced displacement 5 million Afghans fled to Pakistan and Iran, 1/3 of the prewar population of the country, and another 2 million were displaced within the country, making it one of the largest refugee crises in history. In the 1980s, half of all refugees in the world were Afghan. In his report, Felix Ermacora, the UN Special Rapporteur to Afghanistan, enumerated 32,755 killed civilians, 1,834 houses and 74 villages destroyed, and 3,308 animals killed in the first nine months of 1985. Data cited by the World Bank shows that Afghanistan's population declined from 13.4 million (1979) to 11.8 million (1989) during the decade of Soviet occupation.

Maiming and mutilation

In addition to fatalities, 1.2 million Afghans were disabled (Mujahideen, government soldiers and noncombatants) and 3 million maimed or wounded (primarily noncombatants).

Use of chemical weapons There have also been numerous reports of illegal chemical weapons, including mycotoxins, being used by Soviet forces in Afghanistan, often indiscriminately against civilians. Instances include pouring poisonous chemicals into an underground irrigation channel in Padkhwab-e-Shana in 1982; bombs with poisonous gas killing cattle in Qargha and Uzbin; bombs whose explosion shatters chemicals over people's skin, burning it.

Torture