Clément Kayishema was born in 1954 in Bwishyura, Rwanda. In 1974 he was appointed Court Secretary to the Cantonal Tribunal of Kagnagare. One year later he obtained a scholarship grant which allowed him to register for the Faculty of Medicine at the National University of Rwanda in Butare. As soon as his studies were completed, he went into general practice and surgery. In 1984, the Rwandan government sent him to Uganda to practice medicine in a refugee camp. On his return to Rwanda, from 1986 to 1981, he was Director of Nyanza hospital, a position which he held until such time as he was assigned to the Kibuye hospital.
On 3 July 1992, he was appointed Prefet of the Department of Kibuye, and took up this post shortly afterwards. His position was ratified by the interim government in April 1994, just after the death of President Habyarimana. He fulfilled this function as Prefet of Kibuye until his escape to the Democratic Republic of Congo in mid-July 1994. In this position, he represented executive power at the prefectural level. During the 1994 massacres, he wielded both de jure authority and de facto control over the mayors, the gendarmerie and other law enforcement agencies which took part in the massacres.
Towards 14 April 1994, thousands of Tutsis sought refuge in the Mubuga church – situated 20 km from the town of Kibuye – looking for protection from the attacks which were already underway throughout the Kibuye prefecture. Kayishema and his subordinates, amongst whom could be numbered local government officials, gendarmes, units of the communal police and the Interahamwe (extremist Hutu militia), were present at the site and were said to have taken part in the attacks launched against the Mubuga church between 14 and 16 April and which resulted in the deaths of thousands of victims.
On 17 April 1994, Kayishema reportedly took part in the massacre of Tutsis who sought refuge in the grounds of the Catholic Church and the Saint John Home in the town of Kibuye. Here he allegedly played a role of primary importance by leading the assailants from the government offices to the scene of the massacre. Furthermore, it was he who was said to have given the order to attack, led the assault and incited those under his authority to kill, using a megaphone to convey the command from Kigali to kill all of the Tutsis. Kayishema also was said to have orchestrated the burning down of the church and during the full scale attack, stabbed to death a certain Rutabana who was to be found inside this church. This attack, which was reportedly instigated by Kayishema, resulted in thousands of dead and wounded.
On 18 April 1994, thousands of people, for the most part Tutsis, sought refuge inside the stadium in the town of Kibuye. On that same day, Kayishema allegedly went to the stadium and gave the order to units of the gendarmerie, to the local police and to the Interahamwe to attack the stadium. He orchestrated and ordered the assault which he himself led by firing the opening shots at the Tutsis assembled in the Stadium, hitting two of them. These attacks, said to have been instigated by Kayishema, resulted in thousands of dead and wounded.
Kayishema allegedly played a preponderant role in the systematic extermination of the Tutsis who had sought refuge in the Bisesero region located in the Kibuye prefecture. The massacres in the Bisesero region went on for several months, from April to June 1994, and caused tens of thousands of deaths. Transportation of the assailants to the site was assured by buses belonging to the Kibuye prefecture. Kayishema himself reportedly took part in these attacks.
On 13 and 14 April 1994, on the hillside of Muyira, Kayishema was said to have provided the transport for even more assailants, and incited them into attacking those Tutsis who had sought refuge in this area.
At the Kigamara cave in the Bisesero region, where dozens of Tutsis had sought refuge, Kayishema allegedly played a major role in the attack against the Tutsis who had gone into hiding there.
At various other places, Kayishema was said to have escorted units of the gendarmerie and the communal police as well as the Interahamwe militia and armed civilians into the Bisesero region and to have given them orders to attack the Tutsis who had sought refuge there.
In all of these places, it was Kayishema who reportedly drew up the plan of attack, led the charge of the assailants and incited them into perpetrating the massacres.
In the month of July 1994, confronted with the advance of the troops of the RPF (Rwandan Patriotic Front – an opposition movement composed essentially of Tutsi refugees and led by Paul Kagame), Kayishema fled Rwanda in the direction of the Democratic Republic of Congo. On 2 May 1996, he was arrested in Zambia at the request of the Chief Prosecutor of the ICTR (International Criminal Tribunal for Rwanda).