Large-scale control and progressive elimination of a wide variety of parasitic diseases is moving to the fore. Indeed, there is good pace and broad political commitment. Yet, there are some worrying signs ahead, particularly the anticipated declines in funding and coverage of key interventions, and the paucity of novel tools and strategies. Further and intensified research and development is thus urgently required. We discuss advances in epidemiological sampling, diagnostic tools and geospatial methodologies. We emphasise the need for integrating sound epidemiological designs (e.g. cluster-randomised sampling) with innovative diagnostic tools and strategies (e.g. Mini-FLOTAC for detection of parasitic elements and pooling of biological samples) and high-resolution geospatial tools. Recognising these challenges, standardisation of quality procedures, and innovating, validating and applying new tools and strategies will foster and sustain long-term control and eventual elimination of human and veterinary public health issues.