The cost to clover growth of soil-borne root disease was measured in ten New Zealand dairy pasture soils. The average increase clover growth (weight) after soil pasteurisation was 28.5 %, but ranged from a 64 % increase (Whataroa soil) to a decrease of 11.9 % (Ruakura soil). The economic cost of reduced clover growth was determined using the Farmax Dairy Pro decision support system. In Southland and Canterbury, clover root disease was estimated to cost $750 and $715 ha −1 year −1 respectively, and in the Waikato region $1506 ha −1 year −1 . DNA-based testing of the soils detected the presence of diverse fungal, oomycete and nematode pathogen populations. A significant linear relationship was found between reduction in clover growth and group F Pythium spp. (P = 0.0177). The DNA-based assay indicated that Aphanomyces trifolii, a root pathogen of subterranean clover, may be present in the dairy-pasture soils. As this pathogen is currently not recognised as present in New Zealand, a definitive determination of its presence is required. Based on the high economic costs of diseases, the control of soil-borne root pathogens in New Zealand pasture is a direct means to increase profitability.