He was president of the Netherlands Epidemiological Society (1996-1997), a member of the Health Council of the Netherlands (2001-2013), vice-chair and chief methodologist of the Dutch Central Committee on Research involving Human Subjects (2001-2013), chair of the programme committee of the Innovative Medical Devices Initiative (2009-2018), chair of the Netherlands Organisation for Health Research and Development’s Committee for Health Research on Disasters: COVID-19 (since 2021), and chair of the Steering Committee of the Directing Body of Open Science (Open Science NL) of the Dutch Research Council (since 2023).

From 2006 to 2013, he was Rector Magnificus of Vrije Universiteit Amsterdam. In this position, he focused on the formation of interdisciplinary research institutes. As rector, Bouter argued the case for focusing on the societal impact of research and became interested in the dilemmas surrounding research integrity.

In 2014, his tenured professorship was changed from Epidemiology to Methodology and Integrity. He is currently involved in teaching and research in relation to responsible research practices. In 2017, Bouter was appointed a member of the Council for Medical Research of the Royal Netherlands Academy of Arts and Sciences. In 2017, he organized the 5th World Conference on Research Integrity in Amsterdam and became chair of the World Conferences on Research Integrity Foundation. Lex Bouter is the author or co-author of 761 scholarly publications in the Web of Science, which have been cited more than 85,000 times leading to an h-index of 137. He has supervised 78 and currently is supervising 6 PhD students, 17 of whom have been appointed professor to date.