On 23 February, 2006, Ugandan voters could for the first time since 1980 choose a party of their choice rather than select individual candidates within the Nation Resistance Movement (NRM) system. This paper focuses on the role of the Uganda Electoral Commission in administering the 2006 presidential and parliamentary elections. Following international established standards for election monitoring, we asses the administration of the elections through the pre-election, election and post-election stages of the 2006 elections. We also compare the conduct of the 2006 elections to the 2001 elections. Finally, based on observations and key informant interviews, we analyse the perceptions of stakeholders in the electoral process. We find that the current Uganda Electoral Commission improved election management compared to previous elections, but also experienced considerable shortcomings linked to inadequate voter education, significant incumbency advantages and breaches of electoral rules and regulations.