Surveys reveal that the majority of innovation projects do not achieve their goals and waste resources. Notorious examples are the National Health Service's National Programme for IT project and many multibillion European Union funded projects. Academics and practitioners suggest that this failure is because conventional project management methods fail to capture the serendipitous, evolutionary and experimental nature of complex innovation projects. Results from previous research based on European Union healthcare innovation projects revealed that we need to develop a robust method based on the systems thinking construct of equifinality to understand and manage complex causality in projects. This paper critically evaluates how equifinality has been used in management research, the reasons for the discontinuous application of systems thinking and equifinality and examines the ways to embed equifinality in project management, arguing how holism, control, boundary management and causal complexity are critical to the application of system thinking in project management. Copyright © 2012 John Wiley & Sons, Ltd.