Pendidikan Islam : Tradisi dan Modernisasi Menuju Milenium Baru (1999)
Esei-Esei Pendidikan Islam, dan Cendikiawan Muslim (1999)
Renaisans Islam di Asia Tenggara (1999)
Islam Substantif (2000)
Historiografi Islam Kontemporer (2002)
Paradigma Baru Pendidikan Nasional (2002)
Reposisi Hubungan Agama dan Negara (2002)
Menggapai Solidaritas (2002)
Konflik Baru Antar Peradaban (2003)
Islam Nusantara, Jaringan Global dan Lokal (2003)
Surau, Pendidikan Islam Tradisional Dalam Transisi dan Modernisasi (2003)
Shari'a and Politics (2004)
The Origins of Islamic Reformism in Southeast Asia: Networks of Malay-Indonesian and Middle Eastern 'Ulama' in the Seventeenth and Eighteenth Centuries (2004)
Islam in the Indonesian World: An Account of Institutional Formation (2006)
Indonesia, Islam, and Democracy: Dynamics in a Global Context (2006)
Islam Beyond Conflict: Indonesian Islam and Western Political Theory (2008)
Varieties of Religious Authority: Changes and Challenges in 20th Century Indonesian Islam (2010)