Though a historian, he has also focused on the related fields of cultural anthropology and literary studies and pursued topics ranging from language and power, translation and religious conversion, technology and humanity, and the politics and poetics of representation.
In 1993, Duke University Press published Contracting Colonialism: Translation and Christian Conversion in Tagalog Society Under Early Spanish Rule, in which Rafael examined the role of language and translation in the religious conversion of Tagalogs to Catholicism during the early period of Spanish rule of the Philippines.
[3] The Promise of the Foreign: Nationalism and the Technics of Translation in the Spanish Philippines, also published by Duke University Press, appeared in 2005 and is the second volume of Contracting Colonialism.
[4] This book was followed by "Motherless Tongues: The Insurgency of Language Amid Wars of Translation", also published by Duke UP in 2016 which delved into topics ranging from the colonial introduction of English in the Philippines to the fate of interpreters in Iraq during wartime.
Rafael also wrote the introduction to a volume of the works by Nick Joaquin, "The Woman Who Had Two Navels and Tales of the Tropical Gothic" which came out in 2017 from Penguin Classics.