INTRODUCTION Public Health Innovation and Research in Europe (PHIRE), building on previous European collaborative projects, was developed to assess national uptake and impacts of European public health innovations, to describe national public health research programmes, strategies and structures and to develop participation of researchers through the organizational structures of the European Public Health Association (EUPHA). This article describes the methods used. METHODS PHIRE was led by EUPHA with seven partner organisations over 30 months. It was conceived to engage the organisation of EUPHA--working through its thematic Sections, and through its national public health associations--and assess innovation and research across 30 European countries. Public health research was defined broadly as health research at population and organisational level. There were seven Work Packages (three covering coordination and four for technical aspects) led by partners and coordinated through management meetings. RESULTS Seven EUPHA Sections identified eight innovations within the projects funded by the Public Health Programme of the European Commission Directorate for Health and Consumers. Country informants, identified through EUPHA thematic Sections, reported on national uptake of the innovations in eight public health projects supported by the European Union Public Health Programme. Four PHIRE partners, each taking a regional sector of Europe, worked with the public health associations and other informants to describe public health research programmes, calls and systems. A classification was created for the national public health research programmes and calls in 2010. The internal and external evaluations were supportive. CONCLUSIONS PHIRE described public health innovations and research across Europe through national experts. More work is needed to conceptualize and define public health 'innovations' and to develop theories and methods for the assessment of their uptake and impacts at country and cross-country levels. More attention to methods to describe and assess national public health research programmes, strategies and structures--contributing to development of the European Research Area.