The last few decades have seen increasingly widespread use of risk assessment and management techniques as aids in making complex decisions. However, despite the progress that has been made in risk science, there still remain numerous examples of risk-based decisions and conclusions that have caused great controversy. In particular, there is a great deal of debate surrounding risk assessment: the role of values and ethics and other extra-scientific factors, the efficacy of quantitative versus qualitative analysis, and the role of uncertainty and incomplete information. Many of the epistemological and methodological issues confronting risk assessment have been explored in general systems theory, where techniques exist to manage such issues. However, the use of systems theory and systems analysis tools is still not widespread in risk management. This article builds on the Alachlor risk assessment case study of Brunk, Haworth, and Lee to present a systems-based view of the risk assessment process. The details of the case study are reviewed and the authors' original conclusions regarding the effects of extra-scientific factors on risk assessment are discussed. Concepts from systems theory are introduced to provide a mechanism with which to illustrate these extra-scientific effects The role of a systems study within a risk assessment is explained, resulting in an improved view of the problem formulation process The consequences regarding the definition of risk and its role in decision making are then explored.