Understanding the transmission ecology of parasites faces the challenge of studying the complexity of life-cycles at multiple levels of biological organisation and at various space-time scales. We think that a single field of science alone cannot fully address this issue and that a way to understanding such complexity is to connect various fields of science considering the whole transmission system and identifying which are the variables reasonably accessible to measurement and the relevant scales at which they may provide information about transmission processes and indicate a higher risk of transmission/emergence. Based on ongoing studies carried out in Europe and in China, the aim of the present paper is to discuss this system approach and to show how results obtained from mass-screening of human populations may be combined to those obtained from small mammal and landscape ecology studies and modelling to help understanding Echinococcus multilocularis transmission and how differences in the time-space scales at which human infection and small mammal population dynamic processes occur may complicate the analysis.