Parasite requires an understanding of complex transmission systems where individual, population and environmental factors and their interactions can hardly been considered separately. Moreover, the importance of space and time in host population and parasite transmission processes is increasingly recognised. The present review illustrates how epidemiology and transmission ecology have evolved in a multidisciplinary framework to a systems approach that includes both spatial and temporal dimensions. Focusing on population processes, three significant challenges are discussed: (i) integration of landscape ecology concepts and modelling across time-space scales, (ii) development of molecular methods that permits easy parasite/host identification and process tracking (e.g. host and parasite movements), and (iii) integration of sociology methods to estimate zoonotic risk and exposure.