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EFSA guidance regarding pest risk assessment previously identified limitations within a generic qualitative risk assessment scheme published to support EU plant health decision making. In seeking to develop methods to overcome the limitations, we report results of a multiphase project where five test risk assessment methods were applied to Anoplophora glabripennis, Candidatus Phytoplasma pyri, Guignardia citricarpa, Meloidogyne chitwoodi, and Xanthomonas citri strains causing citrus bacterial canker. Teams of pest risk assessors applied the methods to the pests and compared methods in relation to EFSA PLH needs. The most promising method was then revised to incorporate desirable features from the other methods and tested on five more case study pests; Acidovorax citrulli, Ca.P. mali, Ca. P. prunorum, M. Fallax and Mycosphaerella dearnessii. In addition the risk assessment method that emerged from the EU funded project PRATIQUE was adapted to better suit EFSA needs and also tested on the second set of pests. Comprehensive datasheets on each pest were compiled to support the risk assessments. Datasheets included information that emerged from individual pest questionnaires distributed to the National Plant Protection Organisations of each EU Member State. Short term experimental studies were conducted to reduce uncertainty regarding survival and infectivity of the root-knot nematodes in the absence of host plants. Small scale experiments also clarified the role of vectors in the spread of Ca. Phytoplasma prunorum, proving that psyllids acquired the pathogen from wild Prunus sp. and transmitted it to orchards. Results from both sets of studies better informed the respective risk assessments and reduced some uncertainties although significant uncertainties still remain elsewhere within assessments. A novel method to determine an index of individual risk components, e.g. likelihood of entry, was developed. The performance of risk reduction options was evaluated by repeating assessments considering scenarios with and without risk reduction options in place.