[1] He became interested in Protestant evangelism in Latin America and, as an independent researcher, investigated the role of the Summer Institute of Linguistics, focusing on its ties with Evangelical missionary work among the indigenous populations (see Wycliffe Bible Translators), as well as with its possible covert ties with the anti-communist foreign policy of the United States government.
[3] He investigated the role of and impact upon the native Maya Ixil communities of Santa Maria Nebaj of the Guatemalan Civil War, at the peak of its violence in the early 1980s.
There Stoll argued that, contrary to the view then prevalent among foreign observers, the native population of rural Guatemala was never deeply or broadly committed to the leftist guerrillas' armed struggle against the Guatemalan state.
[8][9][10] Stoll's Rigoberta Menchú and the Story of All Poor Guatemalans was re-issued in 2008 in an extended edition with a new foreword by Elizabeth Burgos.
[11] According to Mark Horowitz, William Yaworsky, and Kenneth Kickham, the controversy over Stoll's book on Menchú is one of the three most divisive events in the history of anthropology in the United States, along with controversies about the truthfulness of Margaret Mead's Coming of Age in Samoa and Napoleon Chagnon's representation of violence among the Yanomami.