Here, recent developments in the detection and identification of parasites causing enteric infection are reviewed including the utility and challenges of multi-target molecular assays. Difficulties in clinical interpretation arising from increased detection of parasites, of co-infection with other enteropathogens and of asymptomatic carriage are discussed. Published approaches for detection across a broad range of organisms are described, including commercial assays available to Australian laboratories. Using local data, the impact of introduction of modern molecular assays is assessed. In addition, recent advances in high density multi-target molecular platforms are discussed as potential platforms for increasing the scope of enteric pathogens to be detected whilst maintaining appropriate costs.