In October 2000, Tanzania held its second multi-party general elections. The ruling CCM party's candidate, Benjamin W. Mkapa, defeated his three main rivals, winning the presidential election with 71% of the vote. In the parliamentary elections, CCM won 202 of the 232 elected seats. In the Zanzibar presidential election, Abeid Amani Karume, the son of former President Abeid Karume, defeated CUF candidate Seif Sharif Hamad. The election was marred by irregularities, especially on Zanzibar, and subsequent political violence claimed at least 23 lives in January 2001, mostly on Pemba island. Also, 16 CUF members were expelled from the Union Parliament after boycotting the legislature to protest the Zanzibar election results.

In October 2001, the CCM and the CUF parties signed a reconciliation agreement which called for electoral reforms on Zanzibar and set up a Commission of Inquiry to investigate the deaths that occurred in January 2001 on Pemba. The agreement also led to President appointment of an additional CUF official to become a member of the Union Parliament. Changes to the Zanzibar Constitution in April 2002 allowed both the CCM and CUF parties to nominate members to the Zanzibar Electoral Commission. In May 2003, the Zanzibar Electoral Commission conducted by-elections to fill vacant seats in the parliament, including those seats vacated by the CUF boycott. Observers considered these by-elections, the first major test of the reconciliation agreement, to be free, fair, and peaceful. President Kikwete, Vice President Ali Mohamed Shein, Prime Minister Edward Lowassa, and National Assembly members will serve until the next general elections, which have been set for 2010. Similarly, Zanzibar President Karume and members of the Zanzibar House of Representatives also will complete their terms of office in 2010.