Against the backdrop of terrorist attacks in 1998 and 2002, Kenya has come under pressure from aid donors and diplomatic circles to co-operate in achieving the political and military objectives of the War on Terror. The Kenyan government has received legal, technical and financial support to implement new counter-terrorism structures. However, while these have raised concerns around human rights and the ability of people to come together and organize on shared interests, the response of civil society in Kenya has been muted. It is mainly human rights campaigners, lawyers, Muslim organizations and leaders, and some politicians that have opposed proposed anti-terrorism legislation. Even fewer groups have spoken out against the government's participation in a regional rendition programme in the Horn of Africa supported by the United States. This weak response reflects the significant ethnic and regional fragmentation that prevails in the country. This article critically examines the impacts of counter-terrorism in Kenya and civil society responses to these in a shifting political landscape.