Abstract: Background: Dealing with complex issues per definition bears the burden of imperfection. Whatever comforting theoretical concepts may promise, real life complexity will take its messy toll once travelling from conceptual ambition to real life practice. We specifically reflect on the social scientific contribution to these inter- and transdisciplinary endeavours. Purpose: We reflect on how social scientific research has tried to find its way in complex real life research practice in the field of environment and health and specifically focus on the challenges posed by the imperfections we encountered. Setting: Two case studies in the field of environment and health in Belgium. One case study focuses on policy interpretation of research results. The other focuses on a selection of research priorities. Intervention: Not applicable. Research Design: Not applicable. Data Collection and Analysis: inter- and transdisciplinary research and multi-criteria analysis Findings: Resulting from our practical experiences we present a typology of imperfections: imperfect information, imperfect expert assessment, imperfect processing of incommensurable data, imperfect socio-political weighing/deliberation and reflection on imperfection. As easy as it seems to design processes of structuring complex issues and decision making in which involvement of a relevant diversity of actors and factors is considered praiseworthy, as complicated it is, as we have shown, in practice to organize and live up to expectations. In judging the quality of this endeavour, diverse theoretical yardsticks maybe applied that will not necessarily do justice to the practical complications of research practice. The concepts of abduction, intersubjectivity and transferability, offer interesting qualitative notions of pragmatic approaches that seem relevant to our work.