Compaoré denounced Sankara as a traitor to the revolution and declared his intention to initiate a "rectification" of the revolution. He ruled through the Popular Front, made up of many of the groups that had originally backed Sankara. In early 1988, Compaoré began dismantling some of the governmental structures that Sankara had put in place, starting by replacing the CDRs with revolutionary committees that were, at this point, disarmed. Committees were to be elected by each village, office, factory, and military unit. Local committee members then were to select representatives to serve on regional and national committees. He also began appeals for more private investment, dropped some unpopular taxes, raised the salaries of public officials to generate support among civil servants, and repressed most political opposition through arrest and torture. In 1988, the Popular Front initiated negotiations with the International Monetary Fund (IMF) and the World Bank, a move rejected by the previous government.
Opposition to Compaoré has, at times, come from within the military. In 1988, Compaoré responded to military unrest by ordering the death of several soldiers accused of plotting against the government.
Compaoré has attempted to stabilize a political system historically divided by factionalism among the powerful left-wing organizations and trade unions. However, he has been unable to mobilize widespread popular support for his regime. In April 1989, the government sponsored the creation of the Popular Democratic Organization–Worker's Movement (ODP-MT) in an attempt to unify the many small leftist organizations in the Popular Front. Some progressive leaders strongly against this move were ousted from the Popular Front.
Compaoré's own party formally abandoned Marxism-Leninism in 1991 and endorsed the new Constitution that was accepted by referendum. It provided for a president elected for a seven-year term by universal suffrage and a bicameral national legislature, composed of a 107-member Chamber of Deputies and a 178-member Chamber of Representatives. This latter appointed body, first constituted in 1995, was abolished unanimously by a vote of Parliament in January 2002. (As of 2002, the legislature is comprised of a unicameral 111-member National Assembly.) Following the elections of 5 May 2002, the Congress for Democracy and Progress (CDP) held 57 seats; the African Democratic Rally-Alliance for Democracy and Federation (RDA-ADF) 17; the Party for Democracy and Progress-Socialist Party (PDP-PS) 10; and the Confederation for Federation and Democracy (CFD) 5.
The president appoints the prime minister, who appoints the Council of Ministers. Local government consists of 30 provinces divided into 250 departments, further divided into communes administered by mayors and municipal councils. On 24 September 2000 the CDP won 802 of 1,100 municipal seats, gaining control of 40 of 49 municipalities. The opposition RDA-ADF gained 133 seats. Radical opposition groups boycotted, but altogether 14 parties won seats with a68.4% voter turnout.
Compaoré was successful in his first bid for the presidency in December 1991. He ran uncontested, with opposition parties boycotting the polls. With a low 25% voter turnout, Compaoré was frequently called the "badly elected" president. After opening the political process to other parties, legislative elections were held in 1992. Twenty-seven parties participated, with Compaoré's ODP-MT winning 78 of the 107 seats. The next strongest party won 12 seats.
In February 1996, the CDP, a new pro-Compaoré political party, was formed. The following year, the Compaoré-controlled Assembly approved constitutional amendments that removed restrictions on the renewal of the presidential mandate, allowing Compaoré to run again and increasing the number of parliamentary seats to 111. In 1997 parliamentary elections, 13 political parties and 569 candidates contested for the 111 seats. Compaoré's CDP won 101 seats, further increasing his tight control on the government.
On 15 November 1998, voters were asked to choose between Compaoré and two other contenders. Many observers claimed that the contenders were convinced to run by the president's people in order to legitimize the political process and prevent another unopposed election. A coalition of opposition parties had, as in 1991, called for a boycott. Fifty-eight percent of the electorate turned out, and Compaoré polled 87.53% of the ballots cast, becoming the only Burkinabe president to complete his term of office and be reelected.
In December 1998, the body of Norbert Zongo, editor in chief of an independent weekly newspaper and an outspoken critic of the government, was found, along with the bodies of three of his colleagues, in his burned and bullet-ridden car. Zongo had been investigating the death of Compaoré's brother's driver, David Ouédraogo. At Zongo's funeral 50,000 mourners filled the streets, and rioters looted several cities. Public outcry forced Compaoré to establish an independent investigatory commission and a committee of elders to investigate unpunished political crimes. In August 2000, two presidential guards (including Marcel Kafando, head of the guard) were given prison sentences in connection with the driver's death. In February 2001, Marcel Kafando was charged with arson and the murder of Norbert Zongo and three others, but by March 2002 he was gravely ill in prison. With one of the convicted in the Ouédraogo death already having died in prison, speculation existed that Kafando was being poisoned to silence any eventual confession.