33 candidate applications were registered with the Autonomous National Electoral Commission (CENA). In a ruling issued on January 30 2006, the Constitutional Court accepted 26 of these candidacies. The candidacies of Daniel Shalom, Vincent Emmanuel Ahounou, and Adébayo Ananie were rejected because they were deemed medically unfit for the presidency, while the candidacies of Lary Egoundoukpè and Alidou Tamama were rejected because they had not paid the deposit of five million CFA francs required of candidates. Another two candidates, Edgar Alias and Yaro Sourakatou, withdrew in favor of Boni prior to the ruling. The approved candidates included three serving members of Kérékou's government: Zul Kifl Salami, Antoine Dayori, and Kamarou Fassassi. Additionally, the Constitutional Court approved the candidacies of two heads of major institutions: those of Antoine Idji Kolawolé, the President of the National Assembly, and Raphiou Toukourou, the President of the Economic and Social Council.
In the first round, held on March 5, Boni, former chairman of the West African Development Bank, placed first with about 35% of the vote, and former President of the National Assembly Adrien Houngbédji of the Democratic Renewal Party placed second with about 24% of the vote. In third place was the Social Democratic Party's candidate Bruno Amoussou, a former speaker of parliament and planning minister who obtained about 16% of the vote, and in fourth place was Benin Renaissance candidate Lehady Soglo, son of former president Nicéphore Soglo, with about 8% of the vote. Boni was an independent candidate, and this was his first election; Houngbédji and Amoussou had both run for president three previous times.
Shortly after results were announced in mid-March, the government set the date for the second round between Boni and Houngbédji for March 19. The country's election commission asked for more time, but this was refused. Boni was backed for the second round by both Amoussou and Soglo. He won the second round with almost 75% of the vote and was sworn in on April 6.
The results were as follows:
1) Boni Yayi 1,074,308
2) Adrien Houngbédji 727,239
3) Bruno Amoussou 489,122
4) Léhadi Vinagnon Soglo 253,478
5) Antoine Kolawolé Idji 97,595
6) Lazare Sehoueto 61,195
7) Séverin Adjovi 53,304
8) Antoine Dayori 37,436
9) Kamarou Fassassi 29,494
10) Janvier Yahouedehou 23,054
11) Luc-Marie Constant Gnacadja 20,269
12) Daniel Tawema 18,125
13) Ibrahima Djériwô Idrissou Djarra 18,106
14) Richard Senou 15,672
15) Souley Dankoro 9,929
16) Marie-Elise Gbedo 9,815
17) Célestine Zanou 9,474
18) Lionel Agbo 9,026
19) Zul-Kifl Salami 8,538
20) Richard Adjaho 7,448
21) Gatien Houngbedji 6,544
22) Djimon Hodonou 6,512
23) Galiou Soglo 5,243
24) Kouessan LéandreDjagoue 4,665
25) Marcel Didier Gbaguidi 3,479
26) Raphiou Toukourou 3,419
Eligible Voters: 3,919,550
Voter Turnout: 2,725,634
Votes Cast: 2,656,070
1) Boni Yayi 1,979,305
2) Adrien Houngbédji 673,937